Recent developments in detectors and electronics enable both positron emission tomography (PET) and X-ray computed tomography (CT) data to be acquired concurrently using the same detection front-end for dual-modality PET/CT imaging. Moreover, it would potentially allow substantial reduction of cost and housing size, in addition to facilitating image fusion. However, the lower energy signals (similar to 60 keV versus 511 keV) and higher photon flux per pixel (> 1 Mcps versus 10 kcps) in CT relative to PET cause significant pile-up and dead-time in CT data acquired in photon counting mode. A digital signal processing method was developed and implemented to improve processing of detector signals sampled at low frequency (similar to 45 MHz) in presence of pile-up. The method consists in digitally subtracting the detector impulse response at the output of the preamplifier to restore the signal baseline for more accurate energy estimation. When compared to a fixed threshold counting technique, the proposed method features better noise immunity higher energy resolution and 50% higher rates measured at an estimated true rate of 2.75 Mcps, making CT integration within modern digital PET hardware feasible.