| Year | Title | Role | Notes |
| 1950 | Julius Caesar | Third Plebeian | Uncredited |
| 1951 | Call Me Mister | The Kid | Two minute part. |
| 1951 | Fourteen Hours | Danny Klempner | First film under the contract with Fox. Also stars Grace Kelly in a small role. |
| 1951 | The Frogmen | Pappy Creighton | First featured billing. First film with Robert Wagner. |
| 1951 | Take Care of My Little Girl | Chad Carnes | |
| 1952 | Red Skies of Montana | Edward J. (Ed) Miller | Alternative title: Smoke Jumpers. Billed third. |
| 1952 | Belles on Their Toes | Dr. Bob Grayson | |
| 1952 | Lure of the Wilderness | Ben Tyler | First leading role. |
| 1952 | Dreamboat | Bill Ainslee | |
| 1953 | Sailor of the King | Signalman Andrew 'Canada' Brown | Alternative titles: C.S. Forester's Sailor of the King, Single-Handed.First starring role. |
| 1954 | Three Young Texans | Johnny Colt | First Western. |
| 1954 | Princess of the Nile | Prince Haidi | |
| 1955 | White Feather | Little Dog | |
| 1955 | Seven Angry Men | Owen Brown | Alternative title: God's Angry Man. First film made on loan out to another studio, Allied Artists. |
| 1955 | Seven Cities of Gold | Matuwir | |
| 1955 | The Living Swamp | – | Documentary film. Hunter produced. |
| 1956 | The Great Locomotive Chase | William A. Fuller | Alternative title: Andrews' Raiders |
| 1956 | A Kiss Before Dying | Gordon Grant | Filmed immediately before The Searchers but not released until after. |
| 1956 | The Searchers | Martin Pawley | |
| 1956 | The Proud Ones | Thad Anderson | |
| 1957 | Gun for a Coward | Bless Keough | |
| 1957 | The True Story of Jesse James | Frank James | |
| 1957 | The Way to the Gold | Joe Mundy | |
| 1957 | No Down Payment | David Martin | |
| 1958 | Count Five and Die | Captain Bill Ranson | Shot in Britain. |
| 1958 | The Last Hurrah | Adam Caulfield | Second film for John Ford. |
| 1958 | In Love and War | Sgt. Nico Kantaylis | Last film under contract to Fox. |
| 1959 | La ciudad sagrada | – | Credited as producer; re-released in 1964 as The Mighty Jungle, combined with new African-shot footage with Marshall Thompson |
| 1960 | Sergeant Rutledge | Lt. Tom Cantrell | Last film for John Ford. |
| 1960 | Hell to Eternity | Guy Gabaldon | |
| 1960 | Key Witness | Fred Morrow | |
| 1961 | Man-Trap | Matt Jameson | |
| 1961 | King of Kings | Jesus | |
| 1962 | No Man Is an Island | George R. Tweed | |
| 1962 | The Longest Day | Sgt. (later Lt.) John H. Fuller | Credited as Jeff Hunter |
| 1963 | Gold for the Caesars | Lancer | Alternative title: Oro per i Cesari. Filmed in Italy. |
| 1963 | The Man From Galveston | Timothy Higgins | Pilot for Temple Houston. |
| 1965 | Murieta | Joaquín Murrieta | Alternative title: Joaquín Murrieta |
| 1965 | Uncle Tom's Cabin | | Alternative title: Onkel Toms HütteVoice, Uncredited |
| 1965 | Brainstorm | Jim Grayam | Credited as Jeff Hunter |
| 1966 | Dimension 5 | Justin Power | |
| 1966 | Strange Portrait | Mark | Film never released theatrically. |
| 1967 | A Witch Without a Broom | Garver Logan | Credited as Jeff Hunter |
| 1967 | A Guide for the Married Man | Technical Adviser (Mountain Climber) | Cameo role |
| 1967 | The Christmas Kid | Joe Novak | |
| 1967 | Custer of the West | Capt. Frederick Benteen | |
| 1968 | The Private Navy of Sgt. O'Farrell | Lyman P. Jones | |
| 1968 | Find a Place to Die | Joe Collins | Alternative title: Joe... cercati un posto per morire! |
| 1968 | Sexy Susan Sins Again | Count Enrico | Alternative titles: Frau Wirtin hat auch einen GrafenThe Hostess Also Has a Count |