Draft and minor leagues He was drafted in the sixth round of the
1978 Major League Baseball draft by the Padres out of
Chapman University in
California. Standing at 5'11" tall and weighing 175
lbs., Flannery batted left-handed but threw right-handed. In his first season in the minors (), Flannery batted .350 for the
California League Reno Silver Sox. In , he batted .345 with six
home runs and 71
runs batted in.
San Diego Padres (1979–1989) Flannery received a September call-up to the Majors. Flannery made his Major League debut 26 days before his 22nd birthday, and was the eighth youngest player in the majors in 1979. He batted lead-off and played
second base against the
San Francisco Giants at the Padre's
Jack Murphy Stadium in his first game on September 3, 1979. Flannery was one for three and drove in the second
run of the Padres' 3–0 victory. His minor league success did not translate to major league success as he hit just .154 in 65 big league
at bats, with his only extra base hit of the season being a
triple. He split between the Padres and their triple A affiliate, the
Hawaii Islanders. With Hawaii, Flannery batted .346, however, he hit only .240 in the majors that year. In , he only appeared in 37 games and batted .254. Flannery's first full major league season without spending any time in the minors was . It wasn't until his fifth season, , that Flannery hit his first Major League
home run—a solo shot off the
Chicago Cubs'
Chuck Rainey. Flannery reached the post-season for the only time in his career in . He made three plate appearances in the
1984 National League Championship Series and reached base all three times. Trailing 3–2 in game four of the series, Flannery hit a lead-off
single in the fifth inning, and scored the tying
run of the Padres' 7–5 victory over the Cubs. In game five, he reached on a ground ball that trickled through the legs of Cubs
first baseman Leon Durham to score the tying run. In his only at-bat in the
1984 World Series, Flannery hit an eighth inning
pinch hit single off
Jack Morris in game four. Flannery enjoyed his best year the following season. Having been used all over the infield up to this point in his career, he emerged as the Padres' regular
second baseman in . He batted .281 with 40 RBIs and 50 runs scored—all career highs. He was used as a bench player for the majority of his career. He played his final big league game on his 32nd birthday—September 29, . He spent nine seasons with
Eric Show—longer than any other teammate.
Fan favorite Though never a star, Flannery was a fan favorite in San Diego for much of his career. Team organist Danny Topaz would greet Flannery's plate appearances with the imposing strains of
Wagner's Ride of the Valkyries. His retirement announcement in 1989 resulted in an outpouring of gifts and attention. In his final game, the sellout crowd greeted his first plate appearance with a standing ovation so prolonged that the umpire had to stop play, and following the game, there was discussion on at least one call-in show of whether Flannery's number should be retired. ==Managerial career==