Studies on teacher motivation indicate low teacher motivation results in low student academic performance. The purpose of this study was to determine the relationship between teacher motivation and student academic performance in public secondary schools in Gem Sub-county, Kenya. The objective of the study was to establish the relationship between intrinsic teacher motivation and teacher amotivation on student academic performance. The study was guided by the Conceptual Framework based on Self-Determination Theory and adopted correlation and descriptive research designs. The study population was 41 principals and 180 teachers from 41 public secondary schools. A sample of 36 principals from 36 schools was picked through a saturated sampling technique given that 5 schools were used for the pilot study. The purposive sampling technique was used to select 110 teachers who had taught the same class from form three to form four between 2013-2014. Work Self-Determination Index was used to measure teacher motivation. The reliability of the instruments was established by the test-retest method and a coefficient index of 0.791 was accepted. The study showed that intrinsic teacher motivation had a weak, positive and significant relationship with student academic performance (r =0.327; N=110; p <0.05) and accounted for a 9.9% variation in student academic performance. Teacher amotivation had a weak, positive and significant relationship with student academic performance (r =0.218; N=110; p<0.05) and accounted for a 3.9% variation in student academic performance. The study noted that increased teacher motivation enhances student academic performance. The findings of this study would inform the stakeholders in education in coming up with strategies to enhance teacher motivation to improve student academic performance.