Background Diabetes and hypertension are increasingly prevalent in low and middle income countries, but they are not well documented in refugee settlements in these settings. We sought to estimate the prevalence and associated characteristics of diabetes and hypertension among adults presenting for clinic-based HIV testing in Nakivale Refugee Settlement in Uganda. Methods HIV-negative adults presenting to outpatient clinics for HIV testing at three health centers in Nakivale Refugee Settlement were enrolled from January 2019 through January 2020. Multi-lingual research assistants administered questionnaires aloud to ascertain medical history and sociodemographic information. The research assistants used standardized procedures to measure participants’ blood pressure to detect hypertension (systolic blood pressure ≥ 140 mmHg or diastolic blood pressure ≥ 90 mmHg), and conduct a point-of-care blood glucose test for diabetes (random blood glucose ≥11.1 mmol/L with self-reported frequent urination or thirst, or fasting blood glucose ≥7.0 mmol/L regardless of symptoms), as per Uganda Ministry of Health guidelines. We used χ-square or Fisher’s exact test to test for differences in disease prevalence by refugee status and log-binomial or Poisson regression models to estimate associations of immigration status and country of origin, respectively, with hypertension and diabetes while controlling for age, sex, education level, and body mass index. Results Among 2127 participants, 1379 (65%) were refugees or asylum seekers and 748 (35%) were Ugandan nationals. Overall, 32 participants met criteria for diabetes (1.5%, 95% CI 1.1–2.1%) and the period prevalence was 2.3% (95% CI 1.7–3.0). There were 1067 (50%, 95% CI 48.0–52.2%) who met the criteria for pre-hypertension and 189 (9%, 95% CI 7.7–10.1%) for hypertension. These proportions did not vary by immigration status or country of origin in univariate tests or multivariable regression models. Conclusions Hypertension was common and diabetes was uncommon among those screened in a Ugandan refugee settlement. Routine blood pressure screening should be considered in this setting. Additional research could develop diabetes screening criteria to help identify at risk individuals in this limited resource setting.