Trujillo was drafted in the 7th round (172nd overall) of the 1982 Major League Baseball draft by the Chicago White Sox in the free agent draft. After Trujillo was drafted, it took three years for him to reach the majors.

On September 7, 1984, Trujillo was traded to the San Francisco Giants for Tom O'Malley. He was selected from the Giants by Boston Red Sox in the Rule 5 draft 3 months later.

Trujillo's first career start was in Boston with the Red Sox on April 14, 1985, at the age of 25. As a rookie, he ended the season with an ERA of 4.82 going 4–4. That year, Trujillo recorded 19 strikeouts in 84 full innings pitched while allowing 23 walks and 7 home runs.

During his second year pitching for the Red Sox, he played in three games in the majors, pitching only 5.2 innings. He spent most of 1986 with the Pawtucket Red Sox, where he had a record of 8–9 as a relief pitcher. In August, Trujillo (along with Rey Quiñones, Mike Brown and John Christensen) was traded to the Seattle Mariners. The Red Sox obtained Spike Owen and Dave Henderson.

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