The purpose of this study was to investigate Internal Control System and Financial Management of Government Hospitals in Nigeria. In order to understand the study. A cross sectional survey was employed. Primary data was the source of data collection for this study. An inferential research design and survey method were used for this study, while data collection was adopted using questionnaires administered to 122 122 accountants, internal auditors and procurement or administrative officers of Federal Government Hospitals in Southwest, Nigeria which are Federal Teaching Hospital, Ido – Ekiti, Ekiti State, Nigeria, Federal Medical Center, Owo, Ondo State, Nigeria, University College Hospital, Ibadan, Oyo State, Nigeria, Obafemi Awolowo Teaching Hospital, Ile – Ife, Osun State, Nigeria, Orthopedic Hospital, Gbobi, Lagos State, Nigeria and Federal Medical Centre, Abeokuta, Ogun State, Nigeria. However, data were analyzed by using SSPS. It was found that internal control system positively and significantly influenced financial management of government hospitals in Nigeria. This study therefore, recommended that the management of government hospitals in Nigeria should implement robust control activities such as regular audits and segregation of duties, to ensure accountability and minimize financial mismanagement, they should also foster a strong control environment by promoting ethical leadership, staff training on financial protocols and clear policy enforcement to support effective financial management.