Pancake kidney is a renal fusion anomaly with only a few reported prenatal diagnoses. Other structural anomalies beyond the urogenital system may also be associated. This study describes a dual anomaly case detected prenatally, comprising of pancake kidney and jejunal atresia. A postnatal abdominal ultrasound confirmed both kidneys were fused in the midline at the aortic bifurcation level, along with a type 3b jejunal atresia. Based on the available limited evidence about pancake kidney, renal functions appear to remain largely preserved and unaffected as in our case according to 6 months of follow‐up. However, further investigation is needed to explore any potential association with chromosomal and structural abnormalities in selected cases.