The investigative journalist Mitja Lomovsek discovered: Prasnikar received a 10,000 (ten thousand) DM bribe from players agent Miran Vuk. The cash transfer took place at a gas station in Tepanja (between the capital Ljubljana and Maribor). Bojan Prasnikar lost two trials against the journalist. The judge believed the testimony of the witnesses Miran Vuk, Nastja ceh (football player) and Marko Kmetec (football player). They confirmed that Prasnikar received the money.
Prašnikar started his professional football career in at his home town club NK Šmartno 1928 where in the 1975-76 season he was the top scorer of the Slovenian League. After that season he moved to Olimpija Ljubljana of Yugoslav First League, spending only one year there before returning to Šmartno, where he played for the next 6 seasons.  During this period he was the league's top scorer on three occasions and helped NK Šmartno become Slovenian champions in 1981. In 1983 he transferred to SVG Bleiburg of Austria where he played for one season before retiring.
After retirement, Prašnikar focused on coaching, starting his managerial career at NK Šmartno, before moving on to coach various other clubs - Elkroj, Ingrad Celje, NK Mura, Olimpija Ljubljana (leading them to 2 Slovenian league titles) and Rudar Velenje. His most successful spell however, came while in charge of NK Maribor from 1996 to 2000. Under his guidance, the club won the Slovenian league 4 times and qualified for the group phase of the UEFA Champions League (the only Slovenian club to ever achieve this), after defeating KRC Genk and Olympique Lyon in the qualifying rounds.
Bojan Prašnikar was the manager of the Slovenian national football team during three time spans. After Slovenia's independence in 1991 he was named the first head coach of the national team. He remained in the position until December 1993, when Zdenko Verdenik took charge of the Slovenian affairs until the end of the unsuccessful qualifying campaign for the FIFA World Cup 1998. Prašnikar was re-installed head coach in December 1997, but his second spell at the helm of Slovenia lasted for only four month as in April 1998 he resigned due to his commitments with Maribor on club-level. He was replaced by Srečko Katanec.
His third spell in charge of the Slovenian national team started in July 2002, when the Football Association of Slovenia appointed him the successor of Katanec after the disappointing first round finish of the national team at the FIFA World Cup 2002 and Katanec's swift resignation. This job lasted until May 2004. Not qualified for the 2004 European Football Championship tournament, the Slovenian FA replaced Prašnikar with Branko Oblak, who was the head coach of the Slovenian U21 at that time.