The flipped classroom strategy (FCS) has emerged as an innovative pedagogical approach that enhances active learning, particularly in science subjects like physics. This study investigated the students’ perception of the strategy towards physics instruction. The study adopted mixed research methods, incorporating both qualitative and quantitative data collection techniques. The targeted population of this study was 870 Form One students in secondary schools in Kauma Sub-County. Random sampling was used to sample the schools and students that were involved in the study. The research explored how FCS influences student engagement, conceptual understanding, and achievement in physics. Perception questionnaires were administered to the students after they had undergone the treatment. The questionnaire consisted of closed-ended statements and open-ended questions. The closed-ended section had two sets of statements. The first set was a general statement asking students to indicate whether they perceive the flipped classroom to be a good strategy for physics instruction. The second set consisted of statements that were framed into a Likert-scaled format with five choices illustrating the extent of their agreement with the statements provided. These statements acted as factors that helped to determine the learners’ perception of the flipped classroom towards physics instruction. A total of 84 students answered the questionnaire. MANOVA test was conducted between the perception responses of the students and the students’ responses on the Likert-scaled statements with the help of SPSS 16 and a confidence level of 0.05 to test H03. From the results, the significance level of the MANOVA test was 0.000 for Wilks’ lambda and Roy’s largest root. Since 0.000<0.05, H01 was rejected and the study concluded that students perceived flipped classrooms as an effective strategy for physics instruction. The findings provide insights into the effectiveness of FCS in enhancing physics instruction and offer recommendations for its integration into the Kenyan secondary school curriculum.