The initial response to COVID-19 included quarantine policies. This study aims to determine the infection containment proportions and cost of two variations of quarantine policies based on geographic travel and close contact with infected individuals within deployed US military populations. Special Operations Command Africa (SOCAF) records of individuals quarantined between March 1, 2020 and June 1, 2020 were examined. The infection containment proportion and cost in containment hours were compared between types of quarantine and between geographic areas. Geographic quarantine contained 2 cases out of 63 quarantined individuals in West Africa (3.2%) compared to 0 out of 221 in East Africa (p = 0.0486). Close contact quarantine contained 3 cases out of 31 quarantined individuals in West Africa compared to 4 out of 55 in East Africa (7.3%, p = 0.6989). Total confinement was 42,048 h for each contained infection using geographic quarantine compared to 4076 h using close contact quarantine. In the US military population deployed to Africa for COVID-19, quarantining based on geographic movement is an order of magnitude more costly in terms of time for each contained infection then quarantining based on close contact with infected individuals. There is not a statistical difference between East and West Africa. The associated costs of quarantine must be carefully weighed against the risk of disease spread.