Background: Melatonin may offer a safe and cheap alternative to general anaesthesia and sedatives in neuropaediatric MRI. The purpose of our study was to evaluate its efficacy during a daily scanning programme and to assess its financial benefit. Methods: Neuro-MRI scans, performed in a general hospital setting after administration of melatonin in 64 children aged 10 months–5 years, were retrospectively reassessed by an experienced paediatric neuroradiologist, rating them as diagnostically contributing or as failed. The financial benefit was calculated. Results: 49/64 scans (77%) were diagnostically contributing, in 11 (22%) no movement artefact was seen in any sequence; 15/64 scans failed (23%), in 3/15 because of serious movement artefacts, in 12/15 the scan was not started. Repeat scans under general anaesthesia were performed in 17 cases (27%): in the 15 failed cases and in 2 cases initially assessed as failed, but were considered diagnostically contributing in the present study. The financial benefit at the time the scans were made was approximately 13,360 Euro. Conclusions: In this retrospective study, the use of melatonin in neuropaediatric MRI, made during a daily scanning programme with a remote waiting room, was associated with a high success rate in infants and young children. A minority of scans had no movement artefacts, indicating most children were not asleep. The sleep-inducing effect of melatonin could therefore not be proven, but the high success rate may be attributed to the sedative and/or anxiolytic effect of melatonin. Only a minority of scans had to be repeated under general anesthesia, leading to a reduction of scan related costs.