Advanced-level rural female students perform very poorly in Physics and Mathematics at national examinations in Uganda. Consequently, they fail to get state sponsorship for engineering and technology training in Universities. Hybrid e-learning was introduced for two years in two typical rural girls’ advanced-level secondary schools (Ediofe and Muni) in the rural district of Arua to support the learning and teaching of Physics and Mathematics and was expected to result in an improvement in the achievement scores.. The purpose of this study was to analyze the effects of such an intervention on the achievement scores of the female students in both subjects. Multistage sampling was done to identify 21 participants for Mathematics (11 from Ediofe and 10 from Muni) and another 19 for Physics (12 from Ediofe and 7 from Muni). Six students of Ediofe were offering both Mathematics and Physics while Muni had four such participants. In the hybrid e-learning project, the main course delivery platforms were the training CD-ROMs that were developed based on the requirements of the local curriculum. Senior teachers from Makerere College School, one of the elite advanced level secondary school in Uganda, took part in the development of the content. Additionally, the participating students were allowed access to resources from the Internet from the Faculty of Technology ICT Research Center in Arua town. The Center was set up using the Triple Helix Methodology. External examinations were given to the participating female students in May, June, July and August 2007. The results of these examinations were analyzed as incomplete longitudinal multivariate data. The results of the analysis of the sources of variabilities in performance scores of students show that student level factors were more dominant than school level factors. These results were discussed in light of the Ugandan national policies on rural education.