The study was aimed at evaluating the effectiveness of Instructional Strategies based on Gagne’s Instructional Design and Conventional Strategies of teaching science in improving the Thinking Skills of secondary school students. The seven Thinking Skills suggested by Raths, Louis (1967) namely; Observation; Comparison; Classification; Summarization; Interpretation; Inference and Evaluation were considered. The Pre-test and Post-test Parallel Group, T x L (Treatments x Levels) design was used. A self made Thinking Skills test was used to collect the data from the sample consisting of 96 students studying in standard Eight. Findings of this research revealed that; i) Instructional Strategies based on Gagne’s Instructional Design when compared to that of Conventional Strategies of teaching is significantly effective in improving the Thinking Skills as a Whole and its sub skills namely, Comparison, Summarization, Interpretation, Inference, and Evaluation. ii) Above Average performed significantly better than Average and Average performed significantly better than Below Average in Thinking Skills as a Whole. iii) All the students and at all the three levels, namely, Above Average, Average and Below Average sustained the Thinking Skills improved through Instructional Strategies based on Gagne’s Instructional Design. This study has made an attempt to infuse Thinking Skills into the existing curriculum through Instructional Strategies based on Gagne’s Instructional Design. It has implications for the design and development of Instructional Materials in line with Gagne’s Instructional Design to achieve different learning outcomes. It has been found to be a systematic strategy to improve classroom instruction across various disciplines and hence its inclusion in the teacher education curriculum will be a major step in making its application possible at the grass root level.