Whitney was born in Pasadena, California and attended Pomona College. His first works in film were 8 mm movies of a lunar eclipse which he made using a home-made telescope. In 1937-38 he spent a year in Paris, studying twelve-tone composition under Rene Leibowitz. In 1939 he returned to America and began to collaborate with his brother James on a series of abstract films. Their work, Five Film Exercises (1940–45) was awarded a prize for sound at the First International Experimental Film Competition in Belgium in 1949. In 1948 he was awarded a Guggenheim Fellowship.

During the 1950s Whitney used his mechanical animation techniques to create sequences for television programs and commercials. In 1952 he directed engineering films on guided missile projects. One of his most famous works from this period was the animated title sequence from Alfred Hitchcock’s 1958 film Vertigo, which he collaborated on with the graphic designer Saul Bass.

In 1960, he founded Motion Graphics Incorporated, which used a mechanical analogue computer of his own invention to create motion picture and television title sequences and commercials. The following year, he assembled a record of the visual effects he had perfected using his device, titled simply Catalog. In 1966, IBM awarded John Whitney, Sr. its first artist-in-residence position.