We present a novel joint barcode deblurring and nonuniform illumination compensation algorithm for barcode signals whose number of modules is known. The proposed algorithm is based on a penalized least squares method using a roughness penalty function for an illumination model and a double well penalty function for a barcode signal model. In simulations, the proposed method shows an improved performance compared with a conventional method without compensating nonuniform illumination effects. In addition, the proposed method converges quickly during optimization(within 15 iterations), thereby showing strong possibility for real time decoding of barcode signals.