In the National Basketball Association (NBA), Lynam coached the San Diego / Los Angeles Clippers from 1983 to 1985, the Philadelphia 76ers from 1987 to 1992, and the Washington Bullets from 1995 to 1997.

Lynam won the team MVP award after Jack Egan was expelled for his participation in the 1961 point shaving scandal.

The Hawks then defeated Boston College to advance to the Elite Eight, where their Cinderella run would end by losing to eventual national champion Indiana.

[4] In his second year in Portland, the Blazers won their first playoff series since their championship season of 1976–77, though they would lose in the second round to the Los Angeles Lakers.

[5][6] San Diego native and franchise cornerstone Bill Walton was largely unavailable due to injury and generally frustrated with new Clippers Owner Donald Sterling[7] (Sterling controversially moved the Clippers to Los Angeles overnight, despite not getting approval from the league).

"[13] Lynam's popularity with Sixers players would eventually help him become head coach of the team midway through the 1987–88.

In his second season, Philadelphia won the Atlantic Division title with a 53–29 record, earning the second seed in the conference.

Though finally surpassing the Larry Bird Celtics for the first time in the Charles Barkley-era in Philadelphia, they fell to Michael Jordan's Bulls in back-to-back playoffs.

Barkley was unhappy with team owner Harold Katz over his controversial team decisions,[14] such as trading Moses Malone to Washington, trading the first overall pick in the 1986 NBA draft to Cleveland, and letting Rick Mahorn leave as a free agent among other moves, which were viewed as reasons Philadelphia unraveled from a perennial contender in the 1980s to missing the playoffs in 1992.

[21] Lynam spent two years as Sixers general manager, before accepting an offer to become coach of the Washington Bullets prior the 1994–95 season.

However, on September 29, 2006, it was announced that Lynam, along with NBA hall of famer Moses Malone would be rejoining the 76ers as an assistant coach.

The Minnesota Timberwolves brought in Lynam as a part-time basketball operations consultant, evaluating pro personnel on the Wolves roster and throughout the NBA for part of the 2010–11 season.