Oates was born and raised in Depoy, Kentucky (near Greenville in Muhlenberg County), the son of Sarah Alice (née Mercer) and Bayless E. Oates, who owned a general store. He attended high school in Louisville, and enlisted in the Marines in the 1950s. He began his acting career in New York City starring in a live production of the television series Studio One in 1957.

The actor migrated to Los Angeles where he began to carve out a niche playing guest roles in western television programs of the period including Wagon Train, Tombstone Territory, Rawhide,Trackdown, Wanted: Dead or Alive, Have Gun-Will Travel, The Big Valley and Gunsmoke. Oates first met Peckinpah when he played a variety of guest roles on The Rifleman (1958–1963), the popular television series created by the director. He also played a supporting role in Peckinpah's short-lived TV series The Westerner in 1960. The collaboration continued as he worked on Peckinpah's early films Ride the High Country (1962) and Major Dundee (1965).

In 1961, he guest starred in the episode "Artie Moon" in NBC's The Lawless Years crime drama about the 1920s. In 1962, he appeared as "Ves Painter" in the short-lived ABC series Stoney Burke, co-starring Jack Lord, a program about rodeo contestants. Oates also portrayed a number of memorable characters in guest roles on the enduringly popular television series The Twilight Zone ("The Purple Testament" 1960, "The 7th Is Made Up of Phantoms" 1963, with co-stars Randy Boone and Ron Foster), The Outer Limits ("The Mutant" 1964), Lost in Space ("Welcome Stranger" 1965) and Lancer ("The Man Without a Gun" 1969, "The Buscaderos" 1970).

In addition to Peckinpah, Oates worked with several major film directors of his era including Leslie Stevens in the 1960 film Private Property, his first starring role; Norman Jewison in In the Heat of the Night (1967); Joseph L. Mankiewicz in There Was a Crooked Man... (1970); John Milius in Dillinger (1973); Terrence Malick in Badlands (1973); Philip Kaufman in The White Dawn (1974); William Friedkin in The Brink's Job (1978); and Steven Spielberg in 1941 (1979).

He appeared in the Sherman Brothers musical version of Tom Sawyer as "Muff Potter" the town drunk. He also starred in The Rise and Fall of Legs Diamond (1960), Return of the Seven (1966), The Shooting (filmed in 1965, released in 1968), The Thief Who Came to Dinner (1973), Cockfighter (1974) and China 9, Liberty 37 (1978). Oates co-starred three times with friend Peter Fonda in The Hired Hand (1971), Race with the Devil (1975) and 92 in the Shade (1975).

Oates was cast in Roger Donaldson's 1977 New Zealand film "Sleeping Dogs" together with New Zealand actor Sam Neill. A political thriller with action film elements, 'Dogs' follows the lead character "Smith" (Neill) as New Zealand plunges into a police state as a fascist government institutes martial law after industrial disputes flare into violence. Smith gets caught between the special police and a growing resistance movement and reluctantly becomes involved. Oates plays the role of "Willoughby", commander of the American forces stationed in New Zealand and working with the NZ fascist government to find and subdue 'rebels' (the resistance movement).

His partnership with Peckinpah resulted in two of his most famous film roles. In the 1969 Western classic The Wild Bunch, he portrayed Lyle Gorch, a long-time outlaw who chooses to die with his friends during the film's violent conclusion. According to his wife at the time, Teddy, Oates had the choice of starring in Support Your Local Sheriff, to be filmed in Los Angeles, or The Wild Bunch in Mexico. "He had done Return of the Seven in Mexico; he got hepatitis, plus dysentery. But off he went again with Sam (Peckinpah). He loved going on location. He loved the adventure of it. He had great admiration for Sam. Sam Peckinpah and Monte Hellman were the two directors Warren would work with anytime anywhere." In Bring Me the Head of Alfredo Garcia, the dark 1974 action/tragedy also filmed in Mexico, Oates played the lead role of Bennie, a hard-drinking down-on-his-luck musician hoping to make a final score. The character was reportedly based on Peckinpah himself. For authenticity, Oates wore the director's sunglasses while filming scenes of the production.

Although the Peckinpah film roles are his best-known, his most critically acclaimed role is GTO in Monte Hellman's 1971 cult classic Two-Lane Blacktop. The film, although a failure at the box-office, is studied in film schools as a treasure of the '70s, in large part due to Oates' heartbreaking portrayal of GTO. Famed film critic Leonard Maltin remarked that Oates' performance in this film was as good as any he'd seen and should have won the Oscar.

A year before his death, Oates co-starred with Bill Murray in the 1981 military comedy Stripes. In the role of drill sergeant Sergeant Hulka, Oates skillfully played the straight man to Murray's comedic character. The film was a huge financial success, earning $85 million at the box office. In 1982, he co-starred opposite Jack Nicholson in director Tony Richardson's The Border.

Oates died of a sudden heart attack in Los Angeles, California on April 3, 1982. A few months before his death, he had co-starred in the TV mini-series The Blue and the Gray, which aired in November 1982. His last two films, filmed back-to-back in the months before his death, Blue Thunder and Tough Enough (both released in 1983), were posthumously dedicated to him. Monte Hellman's film Iguana ends with the titles "For Warren" as a dedication. Oates was 53 years old. He was cremated and his ashes scattered in Montana.