Background The Egyptian healthcare system has multiple stakeholders, including a wide range of public and private healthcare providers and several financing agents. This study sheds light on the healthcare system’s financing mechanisms and the flow of funds in Egypt. It also explores the expected challenges facing the system with the upcoming changes. Methods We conducted a systematic review of relevant papers through the PubMed and Scopus search engines, in addition to searching gray literature through the ISPOR presentations database and the Google search engine. Articles related to Egypt’s healthcare system financing from 2009 to 2019 were chosen for full-text review. Data were aggregated to estimate budgets and financing routes. Results We analyzed the data of 56 out of 454 identified records. Governmental health expenditure represented approximately one-third of the total health expenditure (THE). Total health expenditure as a percent of gross domestic product (GDP) was almost stagnant in the last 12 years, with a median of 5.5%. The primary healthcare financing source is out-of-pocket (OOP) expenditure, representing more than 60% of THE, followed by government spending through the Ministry of Finance, around 37% of THE. The pharmaceutical expenditure as a percent of THE ranged from 26.0 to 37.0%. Conclusions Although THE as an absolute number is increasing, total health expenditure as a percentage of GDP is declining. The Egyptian healthcare market is based mainly on OOP expenditures and the next period anticipates a shift toward more public spending after Universal Health Insurance gets implemented.