Fajardo was purchased by the Pittsburgh Pirates from the Mexico City Red Devils on April 2, 1989. He played that season with the Gulf Coast League Pirates. Over the next two seasons, he worked his way through the Pirates organization. Fajardo was nicknamed "Senor Lluvia" or "Mr. Rain" because of how many of the games he was expected to start were rained out.
1991 season
Fajardo had surgery in the off-season to remove bone chips from his arm and his fastball improved significantly, from 85 mph to 93-95 mph. As his fastball and forkball were his main pitches, this marked a key transition. He also threw a curveball and changeup. He pitched at almost every level of the Pirates farm system, leading the club's minor leaguers with 151 strikeouts overall. In a minor-league game in 1991, he broke 9 of opponents bats while pitching. Fajardo played his first games in the major leagues with the Pirates, making his major league debut on August 10. He was traded by the Pirates to the Texas Rangers on September 6, 1991, completing a trade in which Pittsburgh Pirates traded Kurt Miller and a player to be named later to Texas Rangers for Steve Buechele. He appeared in 6 games that season, being the starting pitcher in 5 of those games, recording a 9.95 ERA with Pittsburgh, and a 5.68 ERA with Texas. In total, he struck out 23 batters with 9 earned runs in 25.1 innings pitched.
Fajardo continued to be plagued by injuries in the '93 season, pitching only 2/3 of an inning with the Rangers. He pitched in two games for Charlotte and recorded six starts for the GCL Rangers.
1994 season
1994, his official rookie season, was the year Fajardo finally got a real audition with the Rangers, pitching in the rotation for 3 months, pitching 5-7 with a 6.91 ERA in 18 appearances and 83.1 innings pitched and recording 45 strikeouts. After his time in MLB, he was demoted to the Oklahoma City 89ers, where he was 5–1 with a 2.45 ERA.
1995 season
Like 1991–1993, Fajardo had few appearances in the majors, pitching only 15 innings, and recording a 7.80 ERA. He was traded to the Expos for Lou Frazier. He didn't play with the Expos, and was instantly demoted to the Ottawa Lynx, where he had 11 relief appearance, not recording any decisions, and a 4.11 ERA.
