Her father, Alfred Frankenthaler, was a New York Supreme Court justice. She studied under the Mexican painter Rufino Tamayo (Tamayo, Rufino) in high school, at the Dalton School in New York City, and at Bennington College in Bennington, Vermont. After graduation in 1949, she returned to New York City and studied with painter Hans Hofmann. Influenced by the work of such artists as Arshile Gorky (Gorky, Arshile) and Jackson Pollock (Pollock, Jackson), she eventually became known as a member of the second generation of Abstract Expressionists.

Frankenthaler's first one-woman show was held in New York City in 1951. In one of her major early works, the seminal Mountains and Sea (1952), she created diaphanous colour by means of thinned-down oils that she allowed to soak into the raw (unprimed) canvas. This technique, known as the stain technique, strongly contrasted with the use of impasto that characterized most Abstract Expressionist painting, and it seriously influenced the colour-field painters Morris Louis (Louis, Morris) and Kenneth Noland (Noland, Kenneth).

In the early 1960s Frankenthaler began to use acrylics, and the areas of raw canvas began to assume much greater spatial significance. Her later exhibitions included lithographs and works on paper. Although not abstractions of nature, many of her paintings, such as This Morning's Weather (1982) and Yoruba (2002), embody a strong feeling of landscape. Among her later works are Seeing the Moon on a Hot Summer Day (1987), Warming Trend (2002), and Ebbing (2002).

Frankenthaler taught at a number of universities, including Harvard, Princeton, and Yale. From 1958 to 1971 she was married to the American painter Robert Motherwell (Motherwell, Robert).