The rapid expansion of digital infrastructure across Uganda has created new opportunities to integrate e-learning systems into secondary education, yet significant implementation gaps persist in peri-urban and rural schools. This study documents the design and implementation of an e-learning system at Kabalega Secondary School in Masindi, Uganda, using the Agile Software Development Lifecycle (SDLC) methodology. The system was developed using PHP, MySQL, and JavaScript, incorporating modules for content delivery, student assessment, teacher-student interaction, and progress tracking. System performance was evaluated using the Technology Acceptance Model (TAM), with 180 students and 24 teachers participating in usability and satisfaction surveys over two academic terms. Results indicate that the system achieved a 79.4% user acceptance rate, significantly improved student engagement in assessed subjects, and reduced administrative burden for teachers by 34%. Challenges including intermittent internet connectivity and low digital literacy among older teachers were identified as significant implementation barriers. The study offers a scalable and context-sensitive e-learning implementation framework for similar institutions across Uganda.