In this work, a newly developed reconstruction algorithm, Synchronized MultiArtifact Reduction with Tomographic RECONstruction (SMART-RECON), was applied to C-arm cone beam CT perfusion (CBCTP) imaging. This algorithm contains a special rank regularizer, designed to reduce limited-view artifacts associated with super-short scan reconstructions. As a result, high temporal sampling and temporal resolution image reconstructions were achieved using an interventional C-arm x-ray system. The algorithm was evaluated in terms of the fidelity of the dynamic contrast update curves and the accuracy of perfusion parameters through numerical simulation studies. Results shows that, not only were the dynamic curves accurately recovered (relative root mean square error ∈ [3%, 5%] compared with [13%, 22%] for FBP), but also the noise in the final perfusion maps was dramatically reduced. Compared with filtered backprojection, SMART-RECON generated CBCTP maps with much improved capability in differentiating lesions with perfusion deficits from the surrounding healthy brain tissues.