Born in San Francisco's Castro District, Allen Holubar was the first of five children of Constantin Josef Holubar and Margaret Allen C. Holubar, who immigrated from Bohemia in 1875 and married Margaret, a Scots woman, in San Francisco (Allen was born at 44 Caselli Ave. in a house that still stands). Despite parental pressures to be a machinist, Allen worked his way up from sweeping floors to acting, starting at the Alcazar & Alhambra Theatres in San Francisco. He was evidently a prominent dramatic actor, known widely across the US from 1908-1912. However, in the words of a San Francisco newspaper at the time, "He forsook legitimate drama for the moving picture screen" in 1913. After starring in several landmark films, he began directing and was one of Carl Laemmle's first directors at Universal Pictures. Later, after having differences with Laemmle, he founded his own production company, Allen Holubar Pictures, in 1917.

As an up-and-coming producer, he was famous for being the first to coordinate a movie shoot (Hurricane's Gal (1922)) using radio. In the words of a local paper, "Mr. Holubar has successfully performed the unprecedented task of using the wireless waves to direct the movements of an airship, a destroyer and a schooner, maneuvering all of these within his camera's range as he supervised these activities from a hydroplane far above."

He died of postoperative complications from gallstone surgery at the height of his career in 1923. His wife, the former actress Dorothy Phillips, did not act again until the mid-'60s, when she played an old woman in Cat Ballou (1965), starring Lee Marvin and Jane Fonda.