Delivering sexual and reproductive health education to senior primary school students as they transition into adolescence is crucial. However, implementing such programs in low- and middle-income settings, including regions of China, faces challenges such as untrained educators, cultural sensitivities, and limited educational resources. This study assessed the effectiveness of an online sexual and reproductive health education program designed for senior primary school students, as well as their adherence to the program and comprehension of its content. The trial involved students with an average age of 11 from two primary schools in Shangqiu, Henan Province. Students in the intervention group exhibited significantly greater improvements over time in knowledge, attitudes, and behaviours compared with the control group, as reflected by the significant group × time interaction effects in the GEE models. Results showed that most students in the intervention group successfully completed the program, demonstrated high test scores, and showed significant improvements in their knowledge, attitudes, and behaviors compared to the control group. These gains were sustained at the 16-week follow-up. This study highlights the potential of online education programs to address barriers in delivering sexual and reproductive health education. It also provides a scalable approach and valuable guidance for school health nurses in designing and implementing similar programs in resource-constrained contexts.