Background: Acute pyelonephritis is a bacterial infection of the upper urinary tract. Patients can be admitted to a variety of wards for treatment. However, at the Prince of Wales Hospital in Hong Kong, they are managed initially in the emergency medicine ward. The aim of the study is to identify the risk factors that are associated with a prolonged hospital length of stay. Methods: This was a retrospective cohort study conducted in Prince of Wales Hospital. The study recruited patients who were admitted to the emergency medicine ward between 1 January 2014 and 31 December 2017. These patients presented with clinical features of pyelonephritis, received antibiotic treatment and had a discharge diagnosis of pyelonephritis. The length of stay was measured and any length of stay over 72 h was considered to be prolonged. Results: There were 271 patients admitted to the emergency medicine ward, and 118 (44%) had a prolonged hospital length of stay. Univariate and multivariate analyses showed that the only statistically significant predictor of prolonged length of stay was a raised C-reactive protein (odds ratio 1.01; 95% confidence 1.01–1.02; p < 0.0001). Out of 271 patients, 261 received antibiotics in the emergency department. All 10 patients (8.5%) who did not receive antibiotics in emergency department had a prolonged length of stay (p = 0.0002). Conclusion: In this series of acute pyelonephritis treated in the emergency medicine ward, raised C-reactive protein levels were predictive for prolonged length of stay. Patients who did not receive antibiotics in the emergency department prior to emergency medicine ward admission had prolonged length of stay.