Munari started his career with hometown club Sassuolo, after being promoted to the senior squad from the youth team. He scored 2 goals in 49 appearances during his two-year spell with the club. In 2003, he joined Giulianova, where he would spend just one season, scoring three goals in 25 total appearances. He then joined Serie B side Triestina in 2004 in temporary deal with option to co-own the player. He had an impressive season, making 35 appearances and scoring 5 goals in his only season with the Trieste-based club. In June 2005 Triestina excised the option for €175,000. He was snapped up by another Serie B club on 30 August 2005 in the form of Verona, where he managed to make 38 appearances and score 4 goals in one season. In June 2006 Verona acquired Munari outright from the cross-town rival for an undisclosed fee. Following such an impressive spell in Verona, he was purchased by Serie A side U.S. Città di Palermo together with teammate Mattia Cassani. Half of the Munari's registration rights was valued €1 million while full "card" of Cassani was valued €2.5 million. However, Munari never managed to break into the first team at the Sicilian club and did not play at all during the first half of the 2006–07 Serie A season, being subsequently loaned out to Serie B side Lecce in January 2007. In June 2007 Palermo acquired another half of Munari for €800,000. However, in July 2007, Lecce acquired 50% of the player's rights from Palermo for €1 million; Munari then remained at Lecce for four more seasons, making a total of 143 appearances for the club, scoring 16 goals and becoming one of the first team mainstays.
In June 2011, Munari's co-ownership was ultimately solved in favour of Palermo for €391,000, and the player returned to Palermo, but was immediately clarified he was not in the rosanero first team plans after he was not called up to join the Sicilians' pre-season training camp. On 21 July 2011 he moved permanently to Fiorentina for €800,000, signing a three-year contract for the Tuscans. On 31 January 2012, the final day of 2011-12 winter transfer window, he moved to Serie B side Sampdoria.
After his loan at Watford expired, and after leaving Parma, Munari penned a one-year deal with Cagliari on 29 July 2015. His contract was extended in summer 2016.
Return to Parma
In January 2017, Munari was re-signed by Parma in a 2½-year contract. On 14 November 2019 he announced his retirement from playing and that he joined the club's scouting department.
