BACKGROUND AND PURPOSE: Acquisition of cone-beam CT (CBCT) concurrent with VMAT results in scatter of the megavoltage (MV) beam onto the kilovoltage (kV) detector deteriorating CBCT image quality. The aim of this paper is to develop a method to estimate and correct for MV scatter reaching the kV panel. MATERIAL AND METHODS: The correction method is based on an alternating pulse sequence such that the kV source is enabled in only every other frame. MV scatter, noise and artifacts in the kV-unexposed frames are separated based on their spatial and temporal frequency characteristics and subsequently subtracted from the exposed frames. The method was tested on a phantom and one lung cancer patient scanned on an Elekta Synergy system simultaneous with a 9 Gy VMAT delivery. RESULTS: Without correction, acquisition during VMAT leads to significant cupping and loss of bone contrast. The novel method removes the signal due to MV scatter. Compared to acquisition without MV beam, the reconstruction quality is identical except for some unavoidable noise due to the scattered MV radiation in the exposed frames. Correction is performed in-line with acquisition without introducing delays. CONCLUSIONS: A novel, efficient and effective method was developed to correct for MV scatter in CBCT scans acquired concurrent with rotational radiotherapy.