In 2009, Andújar was the first team goalkeeper in Estudiantes' Copa Libertadores winning team. Andújar did not concede a single goal in any of the eight games in La Plata and he set a new tournament record of 800 minutes without conceding a goal, beating Hugo Gatti's 767 minutes.
On 24 June 2009, Italian club Catania officially announced that the club had signed the player to a four-year deal.
On 24 January 2014, Napoli's official website posted that Andújar was in Naples completing a medical in preparation for his move to the Italian club. Four days later a co-ownership deal was reached with Andújar being loaned back to Catania for the remainder of the season. He will join Napoli at the start of the 2014–15 campaign.