The study employed a descriptive survey to investigate Junior Secondary School Students’ perception of innovative teaching strategies used by teachers in Basic Science and Mathematics. By the use of purposive sampling technique, two hundred (200) students were used as sample size from four selected junior secondary schools in Owerri Municipal Council Area of Imo State. The instrument for data collection was a check-list for teacher’s academic qualification in section A and researcher structured questionnaire in section B with yes/No format. Three (3) research questions and two (2) hypotheses tested at 0.05 level of significance guided the study. The instrument was validated and the reliability index of 0.80 was obtained. The research questions were answered using percentage and proportions while the hypotheses were tested using chi-square statistics. Result showed that teachers of basic science and mathematics do not use innovative strategies during instruction, the proportion of teachers in basic science and mathematics on the use of innovative strategies during instruction is not significant and, gender and academic qualification is not a significant factor in the use of innovative strategies during instruction in basic science and mathematics. Recommendations were–conferences, workshops, and seminars should be organized for the practicing and securing science and mathematics teachers to update their knowledge/skills.