Born in Portland, Oregon, Whalen lived in The Dalles, Oregon from age four until he returned to Portland in 1941. He served in the US Army Air Forces during World War II. He attended Reed College on the GI Bill. There, he met Gary Snyder and Lew Welch, and graduated with a BA in 1951. He read at the famous Six Gallery reading in 1955 that marked the launch of the West Coast Beats into the public eye. He appears, in barely fictionalized form, as the character "Warren Coughlin" in Jack Kerouac's The Dharma Bums (which includes an account of that reading), as well as in later Kerouac novels as "Ben Fagan".
Whalen's first interest in Eastern religions centered on Vedanta. Upon release from the army in 1946, he visited the Vedanta Society in Portland, but did not pursue this very far, because of the expense of attending their countryside ashram. Tibetan Buddhism also attracted him, but he found it "unnecessarily complicated." In 1952, Gary Snyder lent him books on Zen by D. T. Suzuki. Ultimately, Zen became his chosen path.
Whalen spent 1966 and 1967 in Kyoto, Japan, assisted by a grant from the American Academy of Arts and Letters and a job teaching English. There, he practiced zazen daily, and wrote some forty poems and a second novel.
He moved into the San Francisco Zen Center and became a student of Zentatsu Richard Baker in 1972. The following year, he became a monk. He became head monk of Dharma Sangha, in Santa Fe, New Mexico in 1984. In 1987, he received transmission from Baker, and in 1991, he returned to San Francisco to lead the Hartford Street Zen Center until forced by ill health to retire.
His books include You Didn't Even Try (1967), Off the Wall: Interviews with Philip Whalen (1978), Enough Said: 1974-1979 (1980), Heavy Breathing: Poems, 1967-1980 (1983) Two Novels (1986), and Canoeing up Cabarga Creek: Buddhist Poems 1955-1986 (1995). In 1999, Penguin Books published his Overtime: Selected Poems. His Collected Poems were published by Wesleyan University Press in 2007. Both the collected and selected editions were edited by Michael Rothenberg.