We show how splitting supersymmetry reconciles a class of intersecting brane models with unification. The gauge sector in these models arises in multiplets of extended supersymmetry while matter states are in N=1 representations. A deformation of the angles between the branes gives large masses to squarks and sleptons, as well as supersymmetry breaking contributions to other string states. The latter generate at one-loop heavy Dirac masses for Winos and gluinos and can induce a mass term for the Higgsino doublets. We find that this scenario is compatible with gauge coupling unification at high scale for both cases where the gauge sector is N=2 and N=4 supersymmetric. Moreover a neutralino, combination of neutral Higgsinos and Binos, is a natural candidate for dark matter.

10 pages, minor chages, version to be published in PLB