Carboranes are carbon–boron molecular clusters, which can be viewed as three-dimensional analogues to benzene. They are finding many applications in medicine, materials and organometallic chemistry. On the other hand, their exceptional thermal and chemical stabilities, as well as 3D structures, make them very difficult to be functionalized, in particular the regioselective functionalization of BH vertex among ten similar B–H bonds. Here we report a very efficient iridium-catalysed borylation of cage B(3,6)–H bonds of o-carboranes with excellent yields and regioselectivity using bis(pinacolato)diboron (B2pin2) as a reagent. Selective cage B(4)–H borylation has also been achieved by introducing a bulky TBDMS (tert-butyldimethylsilyl) group to one cage carbon vertex. The resultant 3,6-(Bpin)2-o-carboranes are useful synthons for the synthesis of a wide variety of B(3,6)-difunctionalized o-carboranes bearing cage B–X (X=O, N, C, I and Br) bonds.