Perry was signed by the San Francisco Giants on June 3, 1958, for $90,000, which was a big contract at the time. He spent 1958 with the St. Cloud, Minnesota team in Class A Northern League, compiling a 9–5 record and a 2.39 ERA. In 1959 he was promoted to the Class AA Corpus Christi Giants, where he posted a less impressive 10–11 record and 4.05 ERA. He remained with the team as they became the Rio Grande Valley Giants in 1960, and an improved ERA of 2.82 earned him a promotion to the Class AAA Tacoma Giants for the 1961 season. At Tacoma, he led the Pacific Coast League in wins and inning pitched in 1961.