The study investigated the impact of PhET simulation-based learning on students' motivation and academic achievement in learning oscillations and waves among Malawian secondary students. The following research questions guided the study: (i) What were students' motivation and academic achievement levels at the beginning of the study in oscillation and waves? (ii) To what levels do PhET interactive simulation-based learning impact students' motivation and achievement in oscillations and waves? (iii) Is the change in post-test scores due to the students' characteristics in non-randomized settings or the PhET interactive simulation-based learning? A sample of 280 (44.6% females) form three secondary school students with a mean age of 17.5 (SD = 1.424) from four schools in Blantyre urban district in Malawi was used in a quasi-experimental design of non-equivalent groups. The experimental group was exposed to PhET simulation-based learning, while the conventional teaching methods were used in the control group. Pre- and post-tests were used to collect data on academic achievement, and questionnaires collected data on motivation. Independent samples t-test showed a statistical difference between the two groups on post-test of the academic achievement. Results from linear regression indicated that the differences between the two groups in the post-test were not due to students' characteristics but rather the intervention with p < 0.01. The ANCOVA test on motivation constructs showed a significant difference with a small effect size between the study groups on self-efficacy, active learning strategies, performance goals, achievement goals, learning environment stimulation, and attitudes towards learning with computer learning. The results from the study suggest that PhET simulation-based learning improved the learning of oscillations and waves. PhET simulation-based learning provides visualizations and teaching aids that help easily understand content knowledge, hence improving students' academic achievement and motivation levels.