A player who plays in solely defense, Boris started his youth career at Zrinjski Mostar before moving to Široki Brijeg, where he started his professional career. After two-years at the club, Pandža joined Croatian side Hajduk Split in January when the move was completed in late-2006 and the fee was worth about €200,000 on a four and a half year contract. After spending two season limited in the first team, Pandza started to be used more regularly under the management of Ante Miše. On 17 May 2009, Pandza scored his first goal for the club, in a 2–0 victory against Šibenik. After an impressive display at the club, Pandza attracted interests from Premier League side Stoke City. Upon his departure from Hajduk Split, Pandza says he isn't sorry for leaving the club. In July 2010, Pandza joined Belgium side KV Mechelen as a replacement for Jonas Ivens on a three-year contract, with the fee of €350,000. Pandza made his debut for the opening game of the season, in a 2–0 win over Lokeren on 31 July 2010 and then scored his first goal for the club, in a 2–1 win over Zulte Waregem one week after his debut. Pandza then scored his second goal, in a 1–0 win over Standard Liège on 17 September 2010 and third goal came on 1 October 2010, in a 2–2 draw against Genk. In his first full season at the club, Pandza scored four goals in thirty-seven appearance in all competitions. His second season was more enjoyable for Pandza, as he scored the club's first goal of the season, as they beat Sint-Truidense 2-1 on 30 July 2011. He then scored another on 25 January 2012, in a 3–2 win over Genk. In his second season at the club. Pandza scored two goals in thirty-one appearance in all competitions. His last season with the club saw Pandza stayed at the club after his move to Arsenal Kyiv collapsed following a failure to meet the requirement. However, it went appalling for Pandza when he sustained a knee injury, in a 2–0 loss against Beerschot on 1 September 2012 and was out for four weeks. However, it announced furthermore that Pandza will be out for 6 months with an injury that could miss the rest of the season. After having surgery, his knee operated would be a success and will wait for a long time rehabilitation. After three years at the club, Pandza left the club upon his expiry of his contract. Upon leaving Mechelen, Pandza expressed "disappointment" on leaving the club. In July 2013, Pandža was linked with a move to Scottish League One side Rangers. Pandža then began in talks with the club over potentials to join Rangers. Pandža himself pleaded to Rangers, quoting: "come and get him" and even willing to risk his wages. Despite the expected agreement which lasts for two months, the move appeared to be stalled. The move was stalled, which was believed to put on hold by the club's chief executiveCraig Mather and Pandza would later accused the club of lacking professionalism for shattering his move to Rangers. Despite a shattered move to Rangers, Pandža joined Polish side Górnik Zabrze on a one-year contract with an option to extend and will wear number 23 shirt for the club. However, only making thirteen appearance in all competitions, Pandza was released by the club after one season. Pandža returned to NK Siroki Brijeg for the 2014–15 season, making 17 appearances as the club finished in 4th place. The following season, Pandža managed just 9 league appearances.
