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Introduction The Ministry of Public Health in Lebanon is in the process of converting the surveillance reporting from a cumbersome paper-based system to a web-based electronic platform (DHIS-2) to have real-time information for early detection of alerts and outbreaks and for initiating a prompt response. Objectives This paper aimed to document the Lebanese experience in implementing DHIS-2 for the disease surveillance system. It also targets to assess the improvement of reporting rates and timeliness of the reported data and to disclose the encountered challenges and opportunities. Methodology This is a retrospective description of processes involved in the implementation of the DHIS-2 tool in Lebanon. Initially, it was piloted for the school-based surveillance in 2014; then its use was extended in May 2017 to cover other specific surveillance systems. This included all surveillance programs collecting aggregate data from hospitals, medical centers, dispensaries, or laboratories at the first stage. As part of the national roll-out process, the online application was developed. The customized aggregated-based datasets, organization units, user accounts, specific and generic dashboards were generated. More than 80 training sessions were conducted throughout the country targeting 1290 end-users including health officers at the national and provincial levels, focal persons who were working in all public and private hospitals, laboratories, and medical centers as well. Completeness and timeliness of reported data were compared before and after the implementation of DHIS-2. The unveiled challenges and the main lessons learned during the roll-out process were discussed. Results For laboratory-based surveillance, completeness of reporting increased from 70.8% in May to 89.6% in October. Timeliness has improved from 25 to 74%. For medical centers, an improvement of 8.1% for completeness and 9.4% in timeliness was recorded before and after training sessions. For zero reporting, completeness remains the same (88%) and timeliness has improved from 74 to 87%. The main challenges faced during the implementation of DHIS-2 were mainly infrastructural and system-related in addition to poor internet connectivity, limited workforce, and frequent changes to DHIS-2 versions. Conclusion Implementation of DHIS-2 improved timeliness and completeness for aggregated data reporting. Continued on-site support, monitoring, and system enhancement are needed to improve the performance of DHIS-2.