Pergolizzi, a defender, made his professional debut with Sardinian team Olbia Calcio. He then moved to Napoli, where he made a single appearance in the Serie A 1987-1988. Pergolizzi then played for several minor Serie A and B clubs, including Ascoli, Bologna, Brescia, Padova and Ravenna.
He retired in 2001–2002, after a single appearance with Olbia, then in Serie Doctorate.
Pergolizzi started his coaching career in 2002 as Giuseppe Pillon"s assistant coach at Ascoli of Serie C1.
The same year the club immediately gained promotion to Serie B. In 2003–2004 he followed Pillon at Bari. From 2004 to 2005 he coached Serie C2 club Olbia, the same team in which he started and ended his playing career.
In 2005 he was appointed to coach Palermo"s youth squad. In his first season, he reached the semifinals of both the Campionato Nazionale Primavera and the Coppa Italia Primavera.
In 2006–2007, he reached again the Coppa Italia Primavera semifinals, where his team was defeated by Juventus.
On April 23, 2007, following the firing of head coach Francesco Guidolin, Pergolizzi was appointed alongside first team assistant manager Renzo Gobbo to coach Palermo for the five remaining Serie A league matches. He served for only three matches before being sacked himself and replaced by his predecessor Guidolin. After a year without a job, in the summer of 2008 Pergolizzi took back his previous role as Palermo youth team coach.
He left Palermo on June 2010 in order to get back into first team coaching.
In June 2011 he was unveiled as new head coach of Portogruaro, who will take part to the 2011-2012 Lega Pro Prima Divisione after being relegated from Serie B. On July 18, 2011 is forced, in agreement with the company, to leave his post due to serious family problems. On 26 October 2011, he was named head coach of Pavia.
He resigned a few weeks later, on 5 December, due to poor results. On 20 March 2013 he was named new manager of Ascoli, but he was relieved of his duties again on 13 April 2013.