The impact of science teachers' motivation on science students' academic performance in Senior Secondary Schools in Ondo and Ekiti States of Nigeria was investigated in this study. This was a descriptive survey research which was questionnaire based and past WAEC O/L ((May/June 2008 and 2009) student results on the science subjects. The population of the study was all public Secondary Schools (science teachers and students) in Ekiti and Ondo States, Nigeria. A stratified random sampling was used to select a total of five hundred and ten (510) science teachers (male and female) from Ekiti and Ondo States from the selected schools for the study. And a total six thousand eight hundred (6,800) Science Students (male and female) from the selected schools was also considered in the study. In each of the school selected for the study, only teachers of Biology, Chemistry and Physics were involved in the sample and the students that registered and wrote Biology, Chemistry and Physics WAEC examination of May/June 2008 and 2009 in Ekiti and Ondo states of Nigeria. The data collected for the study were analyzed using descriptive analysis, Multiple Regression analysis and Pearson Product Moment Correlation. All the hypotheses were tested at 5 % level of significance. Among others, the study revealed that; there was significant relationship between regular payment of science teachers' allowance and academic performance of science students; there was significant relationship between regular teachers' participation in seminars/ workshops and academic performance of science students. Also, there exist statistical significant relationship between granting of study leave with pay to science teachers and academic performance of science students. As a result of the findings, it was recommended that the adequate science allowance should be regularly paid to the science teachers to enhance their excellent performance.