This systematic review aims to identify the Key Performance Indicators (KPIs) which are the most frequently used and important in the Performance Evaluation (PE) of Health Care Organizations (HCOs). Also, it aimed to analyze the resulted Balanced Scorecard (BSC) dimensions during the Coronavirus Disease 2019 (COVID-19) era. This systematic review was prepared according to PRISMA guidelines. PubMed, Embase, Cochrane, and Google Scholar databases, as well as Google search engine, were inspected to find all implementations of BSC at HCOs until 20 September 2020. The Risk of Bias (RoB) was assessed for each included article. The eligible studies were 33, in which 36 BSC implementations were identified. The categorization and re-grouping of the 797 KPIs resulted in 13 major-dimensions: The financial, efficiency and effectiveness, availability and quality of supplies and services, managerial tasks, Health Care Workers (HCWs) scientific development error-free and safety, the time, HCW-centeredness, patient-centeredness, technology and information system, community care and reputation, HCO building, and the communication. Under them, 45 sub-dimension were identified. The high RoB in most implementations was due to the selection bias. None of the 36 BSC implementations was utilized during the COVID-19 pandemic. This review solves the dilemma of categorization differences among BSC implementations, which in turn will improve the data sharing and comparability among studies. A modification for the BSC design to include external and managerial perspectives is required. However, a lack of a comprehensive PE for HCOs during the pandemic was observed, so the resulted dimensions and KPIs are recommended for planning, monitoring, evaluation, and continuous improvement of HCOs. Many dimensions were negatively influenced by the pandemic. However, some dimensions still need further investigation. BSC dimensions have an essential role in tackling the COVID-19 pandemic and will help the health care managers to mitigate its consequences on HCOs.