He is the brother of former Italian international footballer Amedeo Carboni, who also played for Sampdoria, Roma, and Valencia at club level as a defender.
Carboni played mostly with Tuscan Serie C1 and Serie C2 teams throughout his career in the role of striker, marking his professional footballing debut with hometown club Arezzo in 1980. He then played also for Montevarchi, Empoli and Siena, and retired in 1997 to pursue a coaching career.
Carboni started his coaching career in 1998 with Serie D club Aglianese, leading his side to seventh place in the final standings. In 1999, he left Tuscany to coach Sardinian Serie D side Olbia, ending the season in fourteenth place.
In October 2000 he was surprisingly appointed by Genoa chairman Gianni Scerni to replace Bruno Bolchi at the helm of the rossoblu in the Serie B. Carboni, lacking a valid coaching license for heading a Serie B club, guided the club jointly with veteran manager Alfredo Magni, but was sacked in January 2001 following a poor 17 points in 15 matches.
In 2001-2002, Carboni was appointed at the helm of ambitious Serie C1 side Pisa, but failed to lead the club to a promotion spot, ending the season in a poor tenth place. He returned to Olbia the next season, but obtained an unimpressive fifteenth place in the Serie C2 table and escaped relegation only after playoffs. In 2003, he moved back in Serie C1, at Viterbese, obtaining a third place and allowing the gialloblu to gain a spot in the promotion playoff.
From 2004 to 2006, Carboni coached Bari in the Serie B obtaining a twelfth and a thirteenth final place respectively. After Bari replaced him with Rolando Maran during the summer, he started the 2006-07 season without a job, being appointed on February 2007 as new Crotone boss following the dismissal of Elio Gustinetti in an attempt to avoid relegation which later proved to be unsuccessful. Following Crotone's relegation to Serie C1, Carboni left the Calabrian side, being later appointed at the helm of newly promoted Serie B side Avellino on August 23, 2007, being the third head coach signed by the biancoverdi in the 2007-08 season following resignations by Giovanni Vavassori and successively Maurizio Sarri, all apparingly caused by disputes with the club management. He was sacked on March 2008 due to poor results.
On April 2009 he was appointed to replace Elvio Selighini at the helm of relegation-battling Serie B side Rimini, however failing to save his team from falling down to the lower tier after being defeated to Ancona in the relegation playoffs.
On 25 April 2010, Frosinone announced that Carboni would be the new manager after a poor string of results led to the sacking of Francesco Moriero, leading the club to safety. A poor start in the 2010–11 campaign however led to Carboni's own dismissal later on January 2011.
On 20 November 2011 Carboni becomes the new coach of Empoli in place of the sacked Giuseppe Pillon, until 12 February 2012 when he was sacked.
On 18 January 2013 he was named new coach of Benevento.
In December 2015 he replaced Gianluca Atzori as manager of Siena.