In 1969, the expansion Seattle Pilots signed Bouton and used him almost exclusively out of the bullpen. On May 16, he pitched three innings of hitless, scoreless relief at Fenway Park. The Pilots scored six in the top of the 11th inning to earn him the win, even though other Seattle relievers gave five runs back in the bottom of the 11th. Bouton earned another win in July against the Red Sox with 1 innings of relief, again not allowing a hit. Over 57 appearances with the Pilots, he compiled a 2–1 record with a 3.91 ERA.