Mihajlović made his debut for the first team of Partizan in the last round of 2008–09 season against Čukarički.
After the promotion of Čukarički to Jelen SuperLiga, he has been loaned to Sinđelić Beograd.
Branko Mihajlović signed one year contract with Hapoel Kfar Saba in the summer 2014.
Mihajlović signed for Hapoel Petah Tikva one year contract for 2017–18 season.
After being released from Diósgyőri VTK, he joined FK Mačva Šabac on a free transfer on February 8, 2020.
In the end of June 2022, Mihajlović signed for Enosis Neon Paralimni.
In March 2023, he joined FK Hajduk Divoš, which competes in Vojvodina League South.
In August 2023, he joined OFK Žarkovo, which competes in Belgrade Zone League.