Introduction and objective: Febrile urinary tract infection in a child may be the first manifestation of congenital anomalies of the kidneys and the urinary tract. Renal and bladder ultrasonography remains the first-line imaging modality in children with urinary tract infections. Urinary tract dilation found on ultrasonography prompts further invasive diagnosis; however, when performed in the acute phase of infection, it may potentially reveal misleading findings. Our study investigated whether acute urinary tract infection is associated with urinary tract dilatation and kidney oedema on ultrasonography. Materials and methods: We included 62 children up to 3 years of age with the first episode of febrile urinary tract infection in this prospective cohort study. We performed three ultrasonography examinations in each child: on the first day of the treatment, as well as two and four weeks after treatment onset. We scanned 124 kidneys. Results: The number of kidneys with urinary tract dilation has not significantly changed in consecutive ultrasound examinations. However, both renal length and width increased in the acute phase of urinary tract infection, correlating with symptom duration and C-reactive protein levels, and then subsided within 2–4 weeks. Conclusions: Febrile urinary tract infection does not significantly affect the results of renal and bladder ultrasonography for congenital anomalies of the kidneys and the urinary tract in children up to 3 years old. Kidneys are often involved in children with febrile urinary tract infections. Repeated ultrasound scans before further, more invasive diagnosis are recommended.