Background Despite the clinically apparent congenital urethra anomalies being one of the common causes of admission in pediatric urology, yet little is known about its associated factors, especially in third world countries. Understanding associated factors of clinically apparent congenital urethra anomalies is important in prevention and in genetic counseling that may help in reducing the incidence of their occurrence. Methods Hospital-based cross-sectional prospective study conducted among pediatric patients admitted to pediatric surgery unit at Muhimbili National Hospital from July 2021 to March 2022. Socio-demographic and clinical characteristics were collected from participant’s parent or guardian. Patients were examined thoroughly for clinically apparent congenital urethra anomalies and associated genital-urinary tract anomalies. Analysis was done using SPPS version 23 with descriptive statistics for categorical variables and univariate and multivariate logistic regression for association between presence of clinically apparent urethra anomaly and associated factors at 95% CI. A p-value of < 5 was considered statistically significant. Results Overall proportion of clinically apparent urethra anomaly was 24.4% (94 out of 386) with hypospadias being the commonest anomaly (23.6%); others were epispadias in 2 patients (0.5%) and bladder exstrophy in one patient (0.3%). Among hypospadias cases, sub-coronal (37.4%) and mid-shaft (29.6%) were the most prevalent. About 9.6% had associated anomalies cryptorchidism being the commonest in 8 (8.5%) patients. There was no any factor that was independently associated with development of clinically apparent congenital urethra anomalies. However, folic acid supplementation, maternal hypertension, environmental exposure to pesticides and familial history of congenital urethra anomalies were related to higher proportion of the anomalies despite no any significant relationship detected. Conclusion Hypospadias is the commonest clinically apparent congenital urethra anomalies with cryptorchidism being the most prevalent associated genital-urinary tract anomaly. No associated factor has shown significant relationship with clinically apparent congenital urethra anomalies; however, attention is called to maternal hypertension, environmental exposure, especially pesticides and familial history of congenital urethra anomalies for detailed study. Proper examination of newborns is encouraged for early detection of such anomalies and hence planning for early intervention.