Warner was born, the son of Doreen (née Hattersley) and Herbert Simon Warner, who was a nursing home proprietor. He was born out of wedlock and frequently taken to be raised by each of his parents, eventually settling with his Russian Jewish father and his stepmother. He was educated at Feldon School, Leamington Spa, and trained for the stage at the Royal Academy of Dramatic Art, London.

In 1963, he made his film debut in Tom Jones, and in 1965 starred as Henry VI in the BBC television version of the RSC's The Wars of the Roses cycle of Shakespeare's history plays. Another early television role came when he starred alongside Bob Dylan in the 1963 play The Madhouse on Castle Street.

A major step in his career was the leading role in Morgan: A Suitable Case For Treatment (1966), which established his reputation for playing slightly off-the-wall characters. He also appeared as Konstantin Treplev in Sidney Lumet's 1968 adaptation of Anton Chekov's The Sea Gull

In horror movies he appeared in one of the stories of From Beyond the Grave and opposite Gregory Peck in The Omen (1976) as the ill-fated photojournalist Keith Jennings.

Since then, he has often played villains, in films such as The Thirty-Nine Steps (1978), Time After Time (1979), Time Bandits (1981), Tron (1982), and television series such as Batman: The Animated Series playing Ra's al Ghul, the anti-mutant scientist Herbert Landon in Spider-Man: The Animated Series, as well as rogue agent Alpha in the animated Men in Black series and the Archmage in Disney's Gargoyles and finally The Lobe in Freakazoid.

He was also cast against type as Henry Niles in Straw Dogs (1971) and as Bob Crachit in the 1984 telefilm of A Christmas Carol. In addition, he played Nazi war criminal Reinhard Heydrich in the movie Hitler's SS: Portrait in Evil, and the television mini-series Holocaust.

He has appeared in movies such as Star Trek V: The Final Frontier, Star Trek VI: The Undiscovered Country, Avatar, Teenage Mutant Ninja Turtles II: The Secret of the Ooze (1991), Titanic (the third time he has appeared in a film about RMS Titanic), Scream 2, and more recently in independent television's adaptation of the Hornblower series (which starred Ioan Gruffudd, Warner's co-star on Titanic).

He appeared in three episodes of the second series of Twin Peaks (1991). He also continues to play classical roles. In "Chain of Command", a 6th-season episode of Star Trek: The Next Generation, he was a Cardassian interrogator. He based his portrayal on the evil "re-educator" from 1984.

His less-spectacular roles included a double-role in the campy low-budget fantasy Quest of the Delta Knights (1993) which was eventually spoofed on Mystery Science Theater 3000. He also played Admiral Tolwyn in the movie version of Wing Commander.

On the "nice guy" side, he played the charismatic Aldous Gajic in Grail, a first-season episode of Babylon 5 and Chancellor Gorkon in Star Trek VI: The Undiscovered Country. He also portrayed the sympathetic character of Capt. Kiesel in Sam Peckinpah's Cross of Iron.

In an episode of Lois & Clark he played Superman's deceased Kryptonian father Jor-El, who appeared to his son through holographic recordings. He has also played ambiguous "nice guys" like vampire bat exterminator Philip Payne in 1979's Nightwing; and Dr. Richard Madden in 1994's Necronomicon: Book of the Dead, who had to kill to sustain his life, but was a generally nice person. He also appeared as mad scientist Dr. Alfred Necessiter in the film The Man with Two Brains in 1983 alongside Steve Martin and Kathleen Turner.