Effect of ammonia flow rate on the impurity incorporation and material properties of Si-doped GaN films grown by reactive molecular beam epitaxy (RMBE) process is discussed. It appears that the ammonia flow rate has a marginal effect on the incorporation of impurities into the Si-doped GaN films except there was a little decrease in O and Si with increasing ammonia flow rate when the Si concentration in the film is higher than 1018 cm−3. Electron Hall mobility of Si-doped GaN films grown by RMBE varies with ammonia flow rate used during film growth. From deep level transient spectroscopy (DLTS) measurements for Schottky diodes grown with different ammonia flow rates, one deep trap (C1) particular to the RMBE films was found. The concentration of C1 trap was found to be the lowest in the sample grown with the condition leading to the highest electron Hall mobility within the scope of this experiment. In addition to the DLTS result, other characterization techniques used (x-ray diffraction, cross-sectional transmission electron microscopy, and low-temperature photoluminescence) also consistently show that the RMBE process requires certain value of ammonia flow rate (or V/III ratio if the Ga flux is fixed) to produce Si-doped GaN films with high quality.