He spent two seasons with the Wave. In 1993, he spent the outdoor season with the Tampa Bay Rowdies (APSL). In May 1994, the Washington Warthogs selected Donigan in the Continental Indoor Soccer League draft. The CISL played indoor soccer during the summer and Donigan chose to play for the Rockford Raptors of the USISL instead. That summer, he also signed a three-year contract with the Milwaukee Wave, then backed out of the contract to become an assistant coach at UConn. At the end of the 1996 collegiate season, UConn changed its head coaches and the new coach brought in an entirely new cadre of assistants. Therefore, Donigan decided to resume his playing career. On January 4, 1997, Donigan signed with the Milwaukee Wave for the remainder of the 1996–1997 NPSL season. At the time, he had just moved to St. Louis to become an assistant coach with the St. Louis University men's soccer team. He played XXX seasons with the Wave. Donigan was then hired as an assistant coach with the St. Louis University men's soccer team. As a result, he did not play the beginning of the 1997–1998 season. On January 28, 1998, the Wave traded Donigan to the St. Louis Ambush in exchange for cash, a second-round pick in the 1998 college draft and future considerations. Donigan played parts of two seasons for the Ambush. In May 2000, he signed with the St. Louis Steamers of the World Indoor Soccer League. On September 15, 1990, he earned his only cap with the U.S. national team in a 3–0 victory over Trinidad and Tobago. In 1988, Donigan earned four caps for the United States national futsal team. In 1994 July, Donigan began his coaching career as assistant men's soccer coach at UConn. He would go on to serve as an assistant for three seasons. The college released Donigan in December 1996 after bringing in a new head coach. On February 27, 1997, St Louis University hired Donigan as their assistant coach. On February 5, 2001, the University hired him as its fifth head soccer coach. Donigan won the title of Atlantic 10 Conference Coach of the Year in 2006 and 2007. Dan Donigan was named head coach for the Rutgers men's soccer program on January 22, 2010. Donigan was fired by Rutgers following the 2018 NCAA Division I men's soccer season.