[6] He made his professional debut for the club under Glyn Hodges's caretaker stewardship in a 3–0 defeat to Manchester City at Oakwell on 31 October 2001.

However, he lost his first-team place under Guðjón Þórðarson early in the 2003–04 campaign and was released by Barnsley in October 2003,[8] despite having been offered a new contract just five months earlier.

[13][14] He quickly established himself at the Keepmoat Stadium, but again ran into trouble early into the 2004–05 season, being placed on the transfer list by "Donny" in November 2004.

The utility player was offered a contract by manager Dave Penney in the summer of 2006, but the two sides failed to agree terms.

[18] In June 2006, Mulligan signed for League One side Scunthorpe United, having met manager Brian Laws at a M180 motorway service station to discuss the situation at Glanford Park.

[22] His stay at Vale Park was to prove a relatively short one as manager Lee Sinnott declined to offer Mulligan a longer contract.

[25] He made his debut in the opening round match against Waikato[26] in which he scored two goals in the second half, to give the "Navy Blues" a 3–2 victory.

[27] He played both legs of the 2011 final of the OFC Champions League, as Auckland beat Amicale (Vanuatu) 6–1 on aggregate.

[28] Auckland won the Champions League for a second-successive season in 2012, and this time Mulligan scored one of the goals in a 3–1 aggregate win over AS Tefana (French Polynesia).

[31] Mulligan played for NZ Under-17 at the 1999 FIFA U-17 World Championship and scored two goals in their two pool matches against the United States[32] and Poland.

[37][38] He featured in all six games of the 2008 OFC Nations Cup, which New Zealand won ahead of New Caledonia, Fiji and Vanuatu.

[6] Mulligan was appointed as head coach at Northern League club East Coast Bays in October 2016.