Diabetes mellitus (DM) is increasing markedly in low- and middle-income countries where over three-quarters of global deaths occur due to non-communicable diseases. Unfortunately, these conditions are considered costly and often deprioritized in humanitarian settings with competing goals. Using a mixed methods approach, this study aimed to quantify the cost of outpatient treatment for uncomplicated type-1 (T1DM) and type-2 (T2DM) diabetes at a secondary care facility serving refugees in Kenya. A retrospective cost analysis combining micro- and gross-costings from a provider perspective was employed. The main outcomes included unit costs per health service activity to cover the total cost of labor, capital, medications and consumables, and overheads. A care pathway was mapped out for uncomplicated diabetes patients to identify direct and indirect medical costs. Interviews were conducted to determine inputs required for diabetes care and estimate staff time allocation. A total of 360 patients, predominantly Somali refugees, were treated for T2DM (92%, n = 331) and T1DM (8%, n = 29) in 2017. Of the 3,140 outpatient consultations identified in 2017; 48% (n = 1,522) were for males and 52% (n = 1,618) for females. A total of 56,144 tests were run in the setting, of which 9,512 (16.94%) were Random Blood Sugar (RBS) tests, and 90 (0.16%) HbA1c tests. Mean costs were estimated as: $2.58 per outpatient consultation, $1.37 per RBS test and $14.84 per HbA1c test. The annual pharmacotherapy regimens cost $91.93 for T1DM and $20.34 for T2DM. Investment in holistic and sustainable non-communicable disease management should be at the forefront of humanitarian response. It is expected to be beneficial with immediate implications on the COVID-19 response while also reducing the burden of care over time. Despite study limitations, essential services for the management of uncomplicated diabetes in a humanitarian setting can be modest and affordable. Therefore, integrating diabetes care into primary health care should be a fundamental pillar of long-term policy response by stakeholders.