Born in Borso del Grappa, Magrin began his career with Serie D Bassano Virtus in 1975. He moved to Montebelluna in 1978, where he remained for two seasons. In 1980, he moved to Serie C1 side Mantova, where he remained for one season before moving to newly relegated side Atalanta in 1981. His performances and leadership soon helped the club to achieve Serie A promotion, winning the Serie C title in 1982, and the Serie B title in 1984, in the process. Magrin made his Serie A debut with Atalanta during the 1984–85 season, and later helped the club to the Coppa Italia Final in 1987, where they were defeated by domestic double winners Napoli; in total, he scored 40 goals for Atalanta in 192 appearances.