Background and Aim: In any educational system, academic achievement of students is one of the indicators of success in scientific activities. The aim of this study was to investigate the relationship between motivation and academic achievement of students.Methods: This cross-sectional study included 291 students at Birjand University of Medical Sciences in 2014 which was selected by stratified random sampling method. The instrument used to measure motivation was Academic Motivation Scale (AMS) developed by Valrand et al (1992). Students’ final average grade point was considered as an indicator of academic performance. The data were analyzed in SPSS (version 16) using Pearson correlation test, t-test for independent groups, ANOVA and regression at the significant level a=0.05.Results: The results showed that the intrinsic and extrinsic motivational factors did not have any significant correlation with academic performance. However, nonmotivatedness had a significant relationship with academic performance (P=0.006, r=0.16). The mean score of intrinsic and extrinsic motivation was greater in girls than in boys, while the average score for non-motivatedness was higher in male students than female students (P<0.001). There was also a statistically significant difference in the motivation of students only in terms of their faculty (P=0.003). Motivation and its components mean scores were higher in the freshmen than higher level students (P=0.002, P=0.007, respectively).Conclusions: It is essential, especially on the part of students in health-related disciplines, to identify the size and role of motivation in the academic performance of students in order to carry out educational programs and workshops.