This study examined middle school students’ scientific reasoning ability in relation to gender and learning environment perceptions. The data were obtained from 269 (148 girls and 121 boys) students. A two-tier multiple-choice test was used to assess students’ scientific reasoning ability, while a Likert scale-type self-report questionnaire was used to assess students’ learning environment perceptions. Results showed that there was no significant difference between girls and boys regarding their scientific reasoning abilities. On the other hand, students’ scientific reasoning ability was found to be positively associated with involvement, task orientation, and teacher support, while it was negatively related to cooperation in science learning environments. Since students spent thousands of hours in classrooms, it is vital to examine and deepen the knowledge about the relationship between the learning environment and student outcomes. The current study presented and discussed considering the context of science education in Turkey; further studies can be conducted in different countries and contexts.