Lynam has also served as an assistant coach for several teams, most notably the Sixers and the Portland Trail Blazers, the latter for head coach Maurice Cheeks. When Cheeks was hired as Philadelphia's coach for the 2005–06 season, Lynam was named an assistant. During the preseason, however, he was forced to leave the team due to an undisclosed medical condition. In January 2006, Lynam retired from coaching. 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. In July 2010, The Oregonian reported that Lynam was among candidates for an assistant coaching job in Portland.
On January 24, 2011, the Minnesota Timberwolves announced that Lynam would be joining the club as a part-time basketball operations consultant, evaluating pro personnel on the Wolves roster and throughout the NBA.