Background: To address declining enrolments in science and other STEM subjects in high school and university, particularly disproportionately low enrolments of females in physics, engineering and computer sciences, integrated STEM programs are becoming more popular. However, few studies have investigated classroom experiences or gender differences in the effects of participation in integrated STEM projects on students’ attitudes towards continuing to study STEM subjects. Purpose: This study compared male and female students’ perceptions of classroom emotional climate and their attitudes towards STEM after completing integrated STEM projects. Methods: For a sample of 246 Years 7–10 students participating in integrated STEM projects in 24 co-educational government classrooms, we investigated gender differences using a seven-scale classroom emotional climate questionnaire and an attitude scale. Responses to items in each scale were converted to interval data using Rasch modelling. Differential item functioning between male and female students was investigated and MANOVA was used to compare genders on responses to each scale. Findings: When MANOVA was used to identify gender differences in Rasch student measures of each scale, statistically-significant differences of modest magnitude (0.25–0.50 standard deviations) were found for Clarity, Motivation, Consolidation and Attitudes, but not for Care, Control, Challenge and Collaboration. Relative to males, females had more-negative views for each climate and attitude dimension for which differences were significant. Compared with boys, girls were undermotivated by their STEM projects and perceived less clarity of instruction and feedback. Conclusions: Greater support for female students through clarifying and giving specific feedback on tasks could improve their perceptions of the classroom emotional climate when carrying out integrated STEM projects. Further research is needed to determine the types of projects that motivate females to study STEM.