Brajkovič was signed up as a first year professional but missed the first half of the season due to contractual obligations; he was still contracted with KRKA–Adria Mobil.

Brajkovič started 2006 impressively as well, finishing 4th in the final time trial of Tour de Suisse to take 5th overall in the general classification.

Before that, in the Volta a Catalunya, he took 3rd in the stage 1 time trial, and finished 5th overall just 48 seconds down on race winner David Cañada (Saunier Duval–Prodir).

He did not get to ride the Tour de France, but raced the Vuelta a España where he finished second on the first mountain stage, after getting beaten by Danilo Di Luca in the sprint at the summit.

After finishing fourth in the second mountain stage to the Puerto de El Morredero [es], he took the lead in the general classification, giving him the leader's jersey in a major tour for the first time.

He then endured a dry spell where he further acclimatised to regular top level competition before finishing second to Damiano Cunego at the Giro di Lombardia end of season classic.

During the 2010 season, he won the Critérium du Dauphiné after being able to follow Tour de France champion Alberto Contador in the mountains and besting him in the longer time trial of the race.

[9] In July 2018 the Union Cycliste Internationale (UCI) informed the team about a positive anti-doping test for methylhexanamine recorded by Brajkovič.