In flat-panel detector-based cone-beam computed-tomography breast imaging (CBCTBI) systems, scatter is an important factor that degrades image quality. It has been shown that despite the use of a large air gap, scatter still causes problems when imaging breast phantoms with our CBCTBI prototype. As a result, linear attenuation coefficient (LAC) distortion is obvious in the reconstruction; it appears as cupping artifacts and contrast loss. A simplified beam-stop array (BSA) algorithm is presented in this paper to solve this problem practically and efficiently. When the breast is positioned along the rotational axis, the scatter profiles from different views along a circular orbit are similar, and thus it is possible to use only one x-ray shot with the BSA in place for scatter pattern estimation, and this BSA image is used to generate a scatter pattern for all projections. The result of this scatter correction algorithm is compared with the reconstruction image over a small field of view, where scatter is assumed to be negligible, and the relative reconstruction error (RRE) is evaluated. The reconstruction is not sensitive to the estimation of scatter profile curvature, but is sensitive to the estimation of scatter intensity. It is shown as well that for any angular position where the BSA image is taken, the RRE is very small. The results show that the BSA algorithm works well for our CBCTBI prototype system with almost unchanged x-ray exposure.