The study assessed potential effect of integrated payroll and personnel information system (IPPIS) on the staff payment system in the Nigerian health sector. The study used questionnaire to generate its data. The population of the study comprised only three out of six (6) federal hospitals located in the south-East part of Nigeria, namely; University of Nigeria Teaching Hospital (UNTH), Enugu state with 4,500 staff, Federal Medical Centre, Owerri   Imo state with 3,000 staff and Federal Medical Centre, Umuahia, Abia state with 3,500 staff, making it total population of 11,000.  Two research objectives were employed in this study; (a) to ascertain the extent to which  implementation of  IPPIS has promoted regular payment of salaries (b)to determine the extent to which implementation of IPPIS has ensured total payroll inclusion of all staff. Two (2) hypotheses were tested in line with the objectives.  The sample size was determined at 1,079 (367, 353 and 359) respectively for UNTH, FMC, Owerri and FMC, Umuahia by applying Taro Yamani. The data was analysed through descriptive and inferential statistics and Kruskal-Wallis was used at an alpha level of 0.05.While Duncan post-hoc test was used in cases of difference. The study revealed that IPPIS implementation in the Nigerian health sector has actually promoted regular and prompt payment of salary and ensured inclusion of all staff in the payroll system. The study recommended that the Federal Government of Nigeria should only implement IPPIS in its MDA’s where IPPIS can effectively and efficiently work and also by putting into consideration the peculiarities of such MDA.