Powtoon Software Media Instruction Strategy (PSMIS) is web-based software that allows the establishment of animated presentations and the manipulation of pre-created objects, inserted pictures, music, and edited voice-overs. The study investigates students perceptions of PSMIS and the effect of PSMIS on students academic achievement. The research employed descriptive and quasi-experimental designs. The students’ perceptions were obtained with the instrument Student’s Perception Questionnaire Powtoon Software Media Instruction Strategy (SPQPSMIS), while their academic achievement was obtained with a structured Computer Achievement Test (CAT) with 30 items. A test-retest approach was used for the reliability testing, and a reliability coefficient of 0.81 was achieved using the Kuder-Richardson Formula 20.The sampled population was 85 year three students of computer department FCE(T) Omoku. The students were taught with PSMIS and the traditional lecture method. The obtained data from SPQPSM was analyzed via descriptive statistics with percentage estimation or categorization, the mean and ANCOVA at the .05 level of significance was used to test the academic performance. The findings on perception reveal that 87% of the sampled population has a preference for PSMIS to the lecture method. This is in affirmation of the high academic achievement of the students taught with PSMIS when compared with the lecture method. It is advised that lecturers be prepared with the appropriate ability to use Powtoon Software Media Instruction Strategies (PSMIS) in the classroom.