Objective We determined the malaria prevalence and ascertained the degree of agreement among rapid diagnostic tests (RDTs), urine malaria tests, and microscopy in malaria diagnosis of adults in Nigeria. Methods This was a cross-sectional study among 384 consenting patients recruited at a tertiary health facility in southwestern Nigeria. We used standardized interviewer-administered questionnaires to collect patients’ sociodemographic information. Venous blood samples were collected and processed for malaria parasite detection using microscopy, RDTs, and urine malaria tests. The degree of agreement was determined using Cohen’s kappa statistic. Results The malaria prevalence was 58.3% (95% confidence interval [CI]: 53.0–63.1), 20.6% (95% CI: 16.6–25.0), and 54.2% (95% CI: 49.0–59.2) for microscopy, RDTs, and urine malaria test, respectively. The percent agreement between microscopy and RDTs was 50.8%; the expected agreement was 45.1% and Cohen’s kappa was 0.104. The percent agreement between microscopy and urine malaria tests was 52.1%; the expected agreement was 50.7% and Cohen’s kappa was 0.03. Conclusion The malaria prevalence was dependent on the method of diagnosis. This study revealed that RDTs are a promising diagnostic tool for malaria in resource-limited settings. However, urine malaria test kits require further improvement in sensitivity prior to field use in malaria-endemic settings.