The CO and NOX emissions of strongly pulsed, turbulent diffusion flames were examined experimentally in a co-flow combustor. Video imaging was performed and time-averaged emissions were measured at the combustor exit and near the visible flame tip. Both the case of a fixed fuel injection velocity during the injection interval and a constant fuelling rate were studied for jet Reynolds numbers ranging from 5,000 to 15,000. For fixed injection velocity, maximum emission indices of CO occurred for compact, isolated flame puffs. CO decreased substantially with decreasing jet-off time as the flame puff interaction increased. The pulsed flames had lower NOX than the steady flames, particularly for the case of isolated flame structures. Similar trends in NO formation were seen for constant fueling rate. The CO emissions were, however, considerably different, largely due to a significant impact of the Reynolds number. Radial emissions profiles suggest an improved fuel/air mixing for shorter jet-off times and longer jet-on times. The correlation of CO/NO emissions with a global flame residence time is discussed.