Pulse-modulated generation of atmospheric pressure plasma promises lower operating temperatures and enhanced energy efficiencies compared with those generated using continuous excitation. In this study, the effect of pulse modulation on the ionic content of a radio-frequency helium plasma needle was explored using molecular beam mass spectrometry (MBMS). In all cases reported the pulse repetition frequency was held constant at 6 kHz while the duty cycle and distance between the plasma needle and MBMS were varied from 30% to 90% and 4 mm to 10 mm, respectively. Decreasing the duty cycle was seen to enhance the negative ion flux to the MBMS and yields a clear shift to higher masses for positive ion species. Time-resolved ion intensity measurements (5 µs resolution) demonstrated that negative ions were created almost exclusively in the pulse off-time while positive ions were generated mainly in the on-time. The ions detected were also seen to change as the distance between the sampling orifice and tip of the plasma needle increased, highlighting the effect of different ion mobilities in the flowing gas stream and the presence of an extended cooler afterglow region. The results suggest that there is a possibility of tailoring the ionic plasma chemistry through pulsed modulation, increasing the versatility of the already widely studied plasma needle device.