Theatrical shorts (1938–1964)

• The Night Watchman (1938) (director)
• Dog Gone Modern (1939) (director)
• Robin Hood Makes Good (1939) (director)
• Prest-O Change-O (1939) (director)
• Daffy Duck and the Dinosaur (1939) (director)
• Naughty but Mice (1939) (director)
• Old Glory (1939) (director)
• Snowman's Land (1939) (director)
• Little Brother Rat (1939) (director)
• The Little Lion Hunter (1939) (director)
• The Good Egg (1939) (director)
• Sniffles and the Bookworm (1939) (director)
• The Curious Puppy (1939) (director)
• Mighty Hunters (1940) (director)
• Elmer's Candid Camera (1940) (director)
• Sniffles Takes a Trip (1940) (director)
• Tom Thumb in Trouble (1940) (director)
• The Egg Collector (1940) (director)
• Ghost Wanted (1940) (director)
• Stage Fright (1940) (director)
• Good Night, Elmer (1940) (director)
• Bedtime for Sniffles (1940) (director)
• Elmer's Pet Rabbit (1941) (director)
• Sniffles Bells the Cat (1941) (director)
• Joe Glow, the Firefly (1941) (director)
• Porky's Ant (1941) (director)
• Toy Trouble (1941) (director)
• Porky's Prize Pony (1941) (director)
• Inki and the Lion (1941) (director)
• Snow Time for Comedy (1941) (director)
• The Brave Little Bat (1941) (director)
• Saddle Silly (1941) (director)
• Porky's Midnight Matinee (1941) (director)
• The Bird Came C.O.D. (1942) (director)
• Porky's Cafe (1942) (director)
• Conrad the Sailor (1942) (director)
• Dog Tired (1942) (director)
• The Draft Horse (1942) (director)
• Hold the Lion, Please (1942) (director)
• The Squawkin' Hawk (1942) (director)
• Fox Pop (1942) (director)
• The Dover Boys (1942) (director)
• My Favorite Duck (1942) (director)
• Case of the Missing Hare (1942) (director)
• To Duck or Not to Duck (1943) (director)
• Flop Goes the Weasel (1943) (director)
• Super-Rabbit (1943) (director)
• The Unbearable Bear (1943) (director)
• The Aristo-Cat (1943) (director)
• Wackiki Wabbit (1943) (director)
• Fin'n Catty (1943) (director)
• Inki and the Minah Bird (1943) (director)
• Tom Turk and Daffy (1944) (director)
• Bugs Bunny and the Three Bears (1944) (director)
• The Weakly Reporter (1944) (director)
• Angel Puss (1944) (director)
• From Hand to Mouse (1944) (director)
• Lost and Foundling (1944) (director)
• Odor-able Kitty (1945) (director)
• Trap Happy Porky (1945) (director)
• Hare Conditioned (1945) (director)
• Fresh Airedale (1945) (director)
• Hare Tonic (1945) (director)
• Quentin Quail (1946) (director)
• Hush My Mouse (1946) (director)
• Hair-Raising Hare (1946) (director)
• The Eager Beaver (1946) (director)
• Fair and Worm-er (1946) (director)
• Roughly Squeaking (1946) (director)
• Scent-imental Over You (1947) (director)
• Inki at the Circus (1947) (director)
• A Pest in the House (1947) (director)
• Little Orphan Airedale (1947) (director)
• House Hunting Mice (1948) (director)
• A Feather in His Hare (1948) (director)
• What's Brewin', Bruin? (1948) (director)
• Rabbit Punch (1948) (director)
• Haredevil Hare (1948) (director)
• You Were Never Duckier (1948) (director)
• Daffy Dilly (1948) (director)
• My Bunny Lies over the Sea (1948) (director)
• Scaredy Cat (1948) (director)
• Awful Orphan (1949) (director)
• Mississippi Hare (1949) (director)
• Mouse Wreckers (1949) (director)
• The Bee-Deviled Bruin (1949) (director)
• Long-Haired Hare (1949) (director)
• Often an Orphan (1949) (director)
• Fast and Furry-ous (1949) (director)
• Frigid Hare (1949) (director)
• For Scent-imental Reasons (1949) (director)
• Bear Feat (1949) (director)
• Rabbit Hood (1949) (director)
• The Scarlet Pumpernickel (1950) (director)
• Homeless Hare (1950) (director)
• The Hypo-Chondri-Cat (1950) (director)
• 8 Ball Bunny (1950) (director)
• Dog Gone South (1950) (director)
• The Ducksters (1950) (director)
• Caveman Inki (1950) (director)
• Rabbit of Seville (1950) (director)
• Two's a Crowd (1950) (director)
• Bunny Hugged (1951) (director)
• Scent-imental Romeo (1951) (director)
• A Hound for Trouble (1951) (director)
• Rabbit Fire (1951) (director)
• Chow Hound (1951) (director)
• The Wearing of the Grin (1951) (director)
• Cheese Chasers (1951) (director)
• A Bear for Punishment (1951) (director)
• Drip-Along Daffy (1951) (director)
• Operation: Rabbit (1952) (director)
• Feed the Kitty (1952) (director)
• Little Beau Pepé (1952) (director)
• Water, Water Every Hare (1952) (director)
• Orange Blossoms for Violet (1952) (director)
• Beep, Beep (1952) (director)
• The Hasty Hare (1952) (director)
• Going! Going! Gosh! (1952) (director)
• Mouse-Warming (1952) (director)
• Rabbit Seasoning (1952) (director)
• Terrier Stricken (1952) (director)
• Don't Give Up the Sheep (1953) (director)
• Forward March Hare (1953) (director)
• Kiss Me Cate (1953) (director)
• Duck Amuck (1953) (director)
• Much Ado About Nutting (1953) (director)
• Wild Over You (1953) (director)
• Duck Dodgers in the 24½th Century (1953) (director)
• Bully for Bugs (1953) (director)
• Zipping Along (1953) (director)
• Lumber Jack-Rabbit (1953) (director)
• Duck! Rabbit, Duck! (1953) (director)
• Punch Trunk (1953) (director)
• Feline Frame-Up (1954) (director)
• No Barking (1954) (director)
• The Cat's Bah (1954) (director)
• Claws for Alarm (1954) (director)
• Bewitched Bunny (1954) (director)
• Stop! Look! And Hasten! (1954) (director)
• From A to Z-Z-Z-Z (1954) (director)
• My Little Duckaroo (1954) (director)
• Sheep Ahoy (1954) (director)
• Baby Buggy Bunny (1954) (director)
• Beanstalk Bunny (1955) (director)
• Ready, Set, Zoom! (1955) (director)
• Past Perfumance (1955) (director)
• Rabbit Rampage (1955) (director)
• Double or Mutton (1955) (director)
• Jumpin' Jupiter (1955) (director)
• Knight-mare Hare (1955) (director)
• Two Scent's Worth (1955) (writer & director)
• Guided Muscle (1955) (director)
• One Froggy Evening (1955) (director)
• A Hitch in Time (1955) (director)
• Bugs' Bonnets (1956) (director)
• Broom-Stick Bunny (1956) (director)
• Rocket Squad (1956) (director)
• Heaven Scent (1956) (writer & director)
• Gee Whiz-z-z-z-z-z-z (1956) (director)
• Barbary Coast Bunny (1956) (director)
• Rocket-bye Baby (1956) (director)
• Deduce, You Say (1956) (director)
• There They Go-Go-Go! (1956) (director)
• To Hare Is Human (1956) (director)
• Scrambled Aches (1957) (director)
• Ali Baba Bunny (1957) (director)
• Go Fly a Kit (1957) (director)
• Boyhood Daze (1957) (director)
• Steal Wool (1957) (director)
• What's Opera, Doc? (1957) (director)
• Zoom and Bored (1957) (director)
• Touché and Go (1957) (director)
• Robin Hood Daffy (1958) (director)
• Hare-Way to the Stars (1958) (director)
• Whoa, Be-Gone! (1958) (director)
• To Itch His Own (1958) (director)
• Hook, Line and Stinker (1958) (director)
• Hip Hip-Hurry! (1958) (director)
• Cat Feud (1958) (director)
• Baton Bunny (1959) (director with Abe Levitow)
• Hot-Rod and Reel! (1959) (director)
• Wild About Hurry (1959) (director)
• Fastest with the Mostest (1960) (director)
• Who Scent You? (1960) (director)
• Rabbit's Feat (1960) (director)
• Ready, Woolen and Able (1960) (director)
• Hopalong Casualty (1960) (writer and director)
• High Note (1960) (director)
• Zip 'N Snort (1961) (writer and director)
• The Mouse on 57th Street (1961) (director)
• The Abominable Snow Rabbit (1961) (director with Maurice Noble)
• Lickety-Splat (1961) (writer, director with Abe Levitow)
• A Scent of the Matterhorn (1961) (writer & director, credited as M. Charl Jones)
• Compressed Hare (1961) (director with Maurice Noble)
• Beep Prepared (1961) (writer with John Dunn, director with Maurice Noble)
• Nelly's Folly (1961) (writer with David Detiege, director with Abe Levitow & Maurice Noble)
• A Sheep in the Deep (1962) (writer, director with Maurice Noble)
• Zoom at the Top (1962) (writer, director with Maurice Noble)
• Louvre Come Back to Me! (1962) (director with Maurice Noble)
• Martian Through Georgia (1962) (writer with Carl Kohler, director with Abe Levitow & Maurice Noble)
• I Was a Teenage Thumb (1963) (writer with John Dunn, director with Maurice Noble)
• Now Hear This (1963) (writer with John Dunn, director with Maurice Noble)
• Woolen Under Where (1963) (writer)
• Hare-Breadth Hurry (1963) (director with Maurice Noble)
• Mad as a Mars Hare (1963) (director with Maurice Noble)
• Transylvania 6-5000 (1963) (director with Maurice Noble)
• To Beep or Not to Beep (1963) (writer with John Dunn, director with Maurice Noble & Tom Ray)
• The Iceman Ducketh (1964) (uncredited director with Phil Monroe & Maurice Noble)
• War and Pieces (1964) (director with Maurice Noble)

Television projects

• Gateways of the Mind (1958) (animated sequences directed by Chuck Jones and designed by Maurice Noble)
• The Bugs Bunny Show (1960–62)
• Adventures of the Road Runner (1962) (writer with John Dunn & Michael Maltese, director with Maurice Noble & Tom Ray)
  • This unsuccessful television pilot was later broken up into three theatrical cartoons:
    • To Beep or Not to Beep (released as a theatrical short in 1963)
    • Zip Zip Hooray (Jones not involved)
    • Roadrunner A Go Go (Jones not involved)

Tom and Jerry (1963–1967)

1963

• Pent-House Mouse (producer, writer with Michael Maltese, director with Maurice Noble)

1964

• The Cat Above and The Mouse Below (producer, writer with Michael Maltese, director with Maurice Noble)
• Is There a Doctor in the Mouse? (producer, writer with Michael Maltese, director with Maurice Noble)
• Much Ado About Mousing (producer, director with Maurice Noble)
• Snowbody Loves Me (producer, writer with Michael Maltese, director with Maurice Noble)
• The Unshrinkable Jerry Mouse (producer, writer with Michael Maltese, director with Maurice Noble)

1965

• Ah, Sweet Mouse-Story of Life (producer, writer with Michael Maltese, director with Maurice Noble)
• Tom-ic Energy (producer, writer with Michael Maltese, director with Maurice Noble)
• Bad Day at Cat Rock (producer & writer, director with Maurice Noble)
• The Brothers Carry-Mouse-Off (producer, writer with Jim Pabian)
• Haunted Mouse (producer, writer with Jim Pabian, director with Maurice Noble)
• I'm Just Wild About Jerry (producer, writer with Michael Maltese, director with Maurice Noble)
• Of Feline Bondage (producer, writer with Don Towsley, director with Maurice Noble)
• The Year of the Mouse (producer, writer with Michael Maltese, director with Maurice Noble)
• The Cat's Me-Ouch! (producer, writer with Michael Maltese, director with Maurice Noble)

1966

• Duel Personality (producer, writer with Michael Maltese, director with Maurice Noble)
• Jerry, Jerry, Quite Contrary (producer & writer, director with Maurice Noble)
• Jerry-Go-Round (producer, uncredited director with Abe Levitow & Maurice Noble, the latter of which was also uncredited)
• Love Me, Love My Mouse (producer, director with Ben Washam)
• Puss 'n' Boats (producer)
• Filet Meow (producer)
• Matinee Mouse (uncredited producer)
• The A-Tom-Inable Snowman (producer)
• Catty-Cornered (producer, uncredited director with Abe Levitow, uncredited writer with John Dunn & Michael Maltese, the latter of which was also uncredited)

1967

• Cat and Dupli-cat (producer, writer with Michael Maltese, director with Maurice Noble)
• O-Solar Meow (producer)
• Guided Mouse-ille (producer)
• Rock 'n' Rodent (producer)
• Cannery Rodent (producer & writer, director with Maurice Noble)
• The Mouse from H.U.N.G.E.R. (producer)
• Surf-Bored Cat (producer)
• Shutter Bugged Cat (uncredited producer)
• Advance and Be Mechanized (producer)
• Purr-Chance to Dream (producer, uncredited director with Ben Washam, uncredited writer with Irv Spector & Michael Maltese, the latter of which was also uncredited)

One-shot theatrical shorts

• The Dot and the Line (1965) Oscar winner (producer with Les Goldman, director with Maurice Noble)
• The Bear That Wasn't (1967) (co-producer with Frank Tashlin despite Tashlin having no involvement in the film's production, although he did write the book), director with Maurice Noble

Theatrical features

• Mrs. Doubtfire (1993) (animation opening sequence only; Pudgy & Grunge)

Television series

• Curiosity Shop (1971–72) (executive producer)

Theatrical short films

• Man the Polluter (1973) (animation sequence directed by)

Television specials

Cricket

• The Cricket in Times Square (1973)
• A Very Merry Cricket (1973)
• Yankee Doodle Cricket (1975)

The Jungle Book

• The White Seal (1975)
• Rikki-Tikki-Tavi (1975)
• Mowgli's Brothers (1976)

Raggedy Ann and Andy

• Raggedy Ann and Andy in The Great Santa Claus Caper (1978)
• Raggedy Ann and Andy in The Pumpkin Who Couldn't Smile (1979)

Other

• A Chipmunk Christmas (1981) (character designer and creative consultant, co-produced with Bagdasarian Productions)
• Peter and the Wolf (1995)

Theatrical features

• The Bugs Bunny/Road Runner Movie (1979) (Original bridge animation only)
• Gremlins 2: The New Batch (1990) (animated opening and end credits, featuring Daffy Duck and Bugs Bunny, co-produced with Warner Bros. Feature Animation)
• Stay Tuned (1992) (Robocat segment of Rooney Tunes, co-produced with Warner Bros. Feature Animation)

Theatrical shorts (1994–1997)

• Chariots of Fur (1994) (producer with Linda Jones Clough, writer and director)
• Another Froggy Evening (1995) (producer with Linda Jones Clough, writer with Don Arioli, Stephen A. Fossati, and Stan Freberg, director)
• Superior Duck (1996) (producer with Linda Jones Clough, writer and director)
• Father of the Bird (1997) (producer with Linda Jones Clough)
• Pullet Surprise (1997) (producer with Linda Jones Clough)
• From Hare to Eternity (1997) (producer with Linda Jones Clough, director)

Television series and specials

• The Electric Company (1971) (Wile E. Coyote and Road Runner segments only)
• Bugs and Daffy's Carnival of the Animals (1976) (All-new special featuring Bugs Bunny and Daffy Duck)
• Bugs Bunny in King Arthur's Court (1978) (All-new special featuring Bugs Bunny and Daffy Duck)
• Bugs Bunny's Looney Christmas Tales (1979) (Co-produced by DePatie–Freleng Enterprises)
• Bugs Bunny's Bustin' Out All Over (1980)
• Daffy Duck's Thanks-for-Giving (1980)