Agler began his coaching career with the Columbus Quest in the American Basketball League. In the 1997 season he was elected ABL Coach of the Year. When the league was disbanded after the 1998 season, he moved to the WNBA and was there in the 1999 season, head coach of the Minnesota Lynx, who had just joined the WNBA. He coached the Lynx to the 2002 season, but could not celebrate great successes during this time. In the 2004 season he was the assistant coach of the Phoenix Mercury. From 2005 to 2007 he took the post of assistant coach with the San Antonio Silver Stars.
Since the 2008 season, he has been head coach of the Seattle Storm, with whom he won the WNBA Championship in the 2010 season. In addition, he was selected to the WNBA Coach of the Year 2010.