Students who study science in single-sex and coeducational schools have attracted lots of attention from the education community. However, changes to students' attitudes toward science as they progress to higher grades in these schools are not clearly understood. The aim of this study was to compare the changes in attitudes toward science among lower secondary students (Grade 7 to Grade 9) in single-sex and coeducational schools in Brunei. A cross-sectional survey design was used to collect data from 1,034 students. Despite a significant nonlinear decline in attitudes toward science from Grade 7 to Grade 9, the attitudes remained positive. This decline in attitudes toward science was at a minimum for students in the coeducational school, and it followed the following order: single-sex boys > single-sex girls > coeducational students. The decline was independent of the initial perceived values of the students' attitudes, and it followed different trends when the data of the same-sex students from single-sex and coeducational schools were compared. Male students from the SSB school had more chances for significant decline as they progressed from Year 7 to Year 9. Brunei and countries with similar intentions to expand single-sex and coeducation school systems can target communication between single-sex and coeducation schools so they may learn from each other to improve the effectiveness of science teaching and learning processes. We expect that academics and administrators can benefit from the results of this study to guide their secondary science education policies, curriculum reforms, and teaching practices.