Surface modification of polymers by pulsed plasma has been investigated to minimize degradation reactions occurring at the same time as the surface modification reactions. The hydrogen radical, ion, and electron concentrations in the hydrogen plasma were simulated as a function of the elapsed time after turning off the discharge. The contact angle measurement showed that hydrogen plasma treatment, regardless of pulsed or continuous plasma, led to degradation reactions as well as defluorination and oxidation on PTFE surfaces. The degradation reactions of PTFE chains initiated by the pulsed hydrogen plasma were not as vigorous as those by the continuous hydrogen plasma. A combination of the on-time/off-time of 30/27 mus in the pulsed hydrogen plasma was efficacious in modifying PTFE surfaces.