Los Angeles Clippers (1989–1994)
In his fourth season, 1989–90, after seven games with the Cavaliers, on November 16, 1989, Harper was traded to the Los Angeles Clippers, alongside two first-round draft picks and a second-round draft pick, for Reggie Williams and Danny Ferry, the latter having refused to play for the Clippers.
Harper started all 28 games he played for the Clippers, but his season was cut short by a serious right knee injury suffered in a game in January 1990. Diagnosed with both a torn anterior cruciate ligament and torn cartilage, he underwent surgery.
For the 1989–90 season overall, he averaged 22.8 ppg, 5.9 rpg, 5.2 assists, 2.3 steals and a career-high 1.2 blocks per game. His season was highlighted by back-to-back 39-point games against Denver and Indiana in December 1989, both of which the Clippers won.
In his next season, 1990–91, he was limited to 39 games, but still posted averages of 19.6 ppg and 4.8 rpg along with 5.4 assists and 1.7 steals
By 1991–92, his sixth NBA season, he bounced back to start all 82 games, averaging 18.2 ppg, 5.5 rpg, 5.1 assists and 1.9 steals. as the Clippers advanced to the playoffs, where they were eliminated three games to two by the Utah Jazz.
In 1992–93, Harper was named a co-captain (alongside Danny Manning and Mark Jackson). In 80 games (77 as a starter), Harper averaged 18.0 ppg, 5.3 rpg, 4.5 assists and 2.2 steals. The Clippers again made the playoffs, but yet again Harper's team was eliminated in the first round, this time three games to two by the Houston Rockets.
In 1993–94, his fourth full season with the Clippers and eighth in the NBA, he played and started in 75 games, averaging 20.1 ppg, 6.1 rpg, 4.6 assists and 1.9 steals. On March 11, 1994, he tallied a triple-double with 26 points, 10 rebounds and 10 assists along with six steals in a win over the Dallas Mavericks. Two nights later, he came within one assist of duplicating the feat, with 39 points, 11 rebounds, nine assists plus another six steals in a win over the Golden State Warriors.