This study determined the relationship between scholastic aptitude comprised of reading comprehension, verbal ability, mathematical ability, logical reasoning ability, and visual manipulative skills and Science performance of Grade 9 learners in a privately run basic education institution in Lapu-lapu, Cebu, Philippines during the school year 2015-2016. Descriptive and correlational research designs were carried out to assess the relationship among the identified variables. The study anchored its framework on the Multiple Intelligence Theory and the Primary Mental Abilities Theory. Secondary data on learners’ Science performance, scholastic aptitude and selected demographic profile were considered. Findings revealed a strong association in reading comprehension and Science performance of both sexes between scholar and non-scholar leaners. Moderate direct correlations were noted between learners’ scholastic aptitude pertaining to verbal ability, mathematical ability, logical-reasoning ability and visual manipulative skills, and their science performance. Science performance statistically differed between male and female, and between scholar and non-scholar learners. Female scholar learners performed better than their male non-scholar counterparts in science. In conclusion, scholastic aptitude has bearing on achievement of female scholar learners with respect to their science performance. There is enough evidence to conclude that scholastic aptitude goes hand in hand with science performance. It is imperative then that parents and teachers should work together to develop learners’ scholastic aptitude particularly in reading comprehension to reduce if not eliminate, the sex gap in science performance of learners in the study area. <p> </p><p><strong> Article visualizations:</strong></p><p><img src="/-counters-/edu_01/0770/a.php" alt="Hit counter" /></p>