Kosovo had planned to send three competitors to the AIBA World Championships in Belgrade.
Kosovo's boxing federation has accused Serbia of preventing their team from entering the country for an amateur competition.
Kosovo had planned to send three competitors to the International Boxing Association (AIBA) World Championships in Belgrade.
The boxers tried to cross the border with Serbia on Saturday but were asked not to wear Kosovar emblems on their uniforms.
When they refused and tried to enter Serbia again on Sunday, they were also blocked, according to the Kosovo federation's secretary-general Latif Demolli.
Serbia has not recognised Kosovo's declaration of independence in 2008 and considers it a province.
The AIBA said in a statement that it had contacted Serbian boxing authorities and was trying to resolve the issue.
The authority added that it aimed to "provide a welcoming home for every boxer, and the world of boxing has no borders".
"We believe that all athletes must receive a fair chance to compete and demonstrate their best abilities in the ring,`" the AIBA said. "Sport is intended to unite people and should be free of national politics."
Kosovo is officially recognised by most international sports federations, including FIFA and the International Olympic Committee (IOC).
The European Commission spokesperson Peter Stano said on Wednesday that Kosovo's Boxing Association should "be allowed to participate on an equal footing".
German Ambassador to Kosovo, Jörn Rohde, also wrote on Twitter that "politicising sport is never a good idea," while Albania’s national team also threatened to quit the championship over Kosovo's treatment.