Charles also spent several years as coach of the US U23 men's national team, culminating with the 2000 Summer Olympics. During this period, Charles was battling prostate cancer, but continued to coach the US to a fourth-place finish in the games. He retired from coaching the U23 team after the Olympics, with a record of 23–11–13 (.628). He also coached the team to a bronze medal at the 1999 Pan American Games and third place at the 1997 World University Games. He served as an assistant coach of the United States men's national soccer team in the 1998 World Cup.