In response to the leaky STEM pipeline, particularly for girls, many schools have introduced integrated STEM (iSTEM) programs to enable students to solve problems using skills from each STEM area and hopefully enhance their interest in continuing with STEM subjects in senior-high school and university. We investigated whether gender differences in students’ perceptions of classroom emotional climate and attitudes to STEM depend on whether students are undertaking iSTEM projects as part of a multidisciplinary curriculum (S, T, E and M) or unidisciplinary curriculum (S, T, E or M) and also whether they attend a government or nongovernment coeducational school. The sample consisted of 256 students in 24 coeducational grade 7–9 classes in 8 government schools and 157 students in 12 coeducational grade 7–10 classes in 6 nongovernment schools. Whereas boys were significantly more positive than girls in perceptions of clarity, motivation, consolidation and attitudes to iSTEM in coeducational government schools, there were no significant gender differences in coeducational nongovernment schools. Students of both genders in government schools were significantly more positive about all aspects of classroom emotional climate and attitudes than students of both genders in nongovernment schools, even after controlling for socioeconomic status. Also, females were slightly more positive about classroom emotional climate and in their attitudes in multidisciplinary STEM classes in government schools. This study suggests that multidisciplinary STEM classes could motivate girls to pursue STEM subjects in senior-high school and at university.