This study investigated the effectiveness of simulation-based instruction on students’ greenhouse effect achievement. The simulations were chosen from the Physics Education Technology Project (PhET) website. The research was a pretest-posttest with a control group design quasi-experimental study. The sample of the study consisted of 45 6th grade students taking a science course in a secondary school from a city located in the Central Anatolia Region of Turkey in the 2017–2018 academic year. Participants were assigned randomly to control and experimental groups. There were 23 participants in the experimental group and 22 participants in the control group. While the control group was instructed with the constructive instructional methods, the experimental group was instructed by PhET simulation-based instruction over 1 week. Data were collected by the Greenhouse Effect Achievement Test. Independent samples t-test and paired samples t-test were used to analyze the data. The study results revealed that the PhET simulation-based instruction created a statistically significant difference between the control group and the experimental group in the students’ greenhouse effect in favor of the experimental group (p = 0.03).