The Philippine health system has undergone various changes which addressed the needs of the time. These changes were reflected in the benchmarks and indicators of performance of the whole health system. To understand how these changes affected the health system (HS), this study determined the changes in the Philippine health system in relation to different health domains (health determinants, financing, and management/development). Two HS periods were identified, namely, health system period 1 (HS 1) from 1997–2007 and health system period 2 (HS 2) from 2008–2017. Each HS period was assessed based on three domains. The first two domains were quantitatively assessed based on an interrupted time-series method, while the third one underwent a comparative analysis using two Health Systems in Transition reports (2011 and 2018). This study was able to assess the developmental changes in the Philippine health system. Specifically, the (health determinant) maternal mortality rate (MMR) significantly decreased by three maternal deaths per 100,000 live births, the (health financing) tobacco excise tax increased by 13,855 (in Million PhP) in HS 2, and there was (health management/development) an improvement in access to health facilities. However, there was an indication of retrogressive progress with some challenges in HS 1 which remained unaddressed in HS 2. While it seems promising that the health system has progressed with improvements apparent in both health outcomes (e.g., MMR) and health financing (e.g., tobacco excise tax), such improvements were overshadowed by the inefficiencies, which were not addressed by the current health system (HS 2), thus making it more retrogressive than progressive.