Background: The Health Information System (HIS) is a set of computerized tools for the collection, storage, management, and transmission of health data. The role of such tools in supporting the modernization of health systems, improving access to quality healthcare, and reducing costs in developing countries is unquestionable, but their implementation faces several challenges. In Gabon, a unique national electronic HIS has been launched. It will connect healthcare institutions and providers at all levels in the whole country. Objective: This study aims to explore and identify the factors influencing healthcare providers' perceptions of the national electronic HIS in Gabon. Methods: A 44-item questionnaire based on the Information System Success Model (ISSM) was administered between February and April 2018 among 2600 healthcare providers across the country. The questions assessed the different aspects of the HIS that could influence its perceived impact on a 5-level Likert scale (from fully agree to totally disagree). The reliability and construct validity of the questionnaire were checked using Cronbach alpha and congeneric reliability coefficients. A logistic regression was used to identify the factors influencing healthcare providers' perceptions of the system. Results: A total of 2327 questionnaires were completed (i.e. 89.5% response rate). The logistic regression identified five elements that significantly influenced perceived system impact: System Quality (Odds Ratio-OR = 1.70), Information Quality (OR = 1.69), Actual Use (OR = 1.41), Support Quality (OR = 1.37), and Useful Functions (OR = 1.14). The model explained 30% of the variance in providers' perception that the national HIS leads to positive impacts.