Background: Motivation is an intrusive force that leads individuals physiologically and psychologically to pursue their goals to meet their needs and expectations. Considering the importance of motivation in the health sector, this study aimed to prioritize the effective factors on staff motivation in Rafsanjan University of Medical Sciences. Methods: This is a descriptive-analytic study that was conducted in a cross-sectional fashion in 2016 on 222 staff members of Rafsanjan University of Medical Sciences who were selected by stratified random sampling method. A researcher-made questionnaire comprised of 40 questions in 11 dimensions including salary, policy, occupational safety, environmental conditions, supervision and support, appreciation, job development, the nature of work, job responsibility, occupation, and communication was used to collect data. The TOPSIS and SPSS 21 software were used to analysze data. Results: There was a significant relation between education level and motivation, but there were no significant relations between age, employment status, and career path and motivation. Also, the results of ranking the options indicated that the communication option with (0. 74%) had the highest priority and the appreciation option with (0. 29%) had the least priority in motivational factors. Conclusion: Since communication in this study was the most important among the motivational factors of the employee staff, it is suggested that managers develop a sense of trust and friendship between management and employees through facilitating and expanding vertical communication in order to increase motivation among employee staff.