Background Patients in the Neonatal Intensive Care Unit (NICU) are at an increased risk for medication errors. Objective The objective of this study is to describe the nature and setting of medication errors occurring in patients admitted to an NICU in Qatar based on a standard electronic system reported by pharmacists. Setting Neonatal intensive care unit, Doha, Qatar. Method This was a retrospective cross-sectional study on medication errors reported electronically by pharmacists in the NICU between January 1, 2014 and April 30, 2015. Main outcome measure Data collected included patient information, and incident details including error category, medications involved, and follow-up completed. Results A total of 201 NICU pharmacists-reported medication errors were submitted during the study period. All reported errors did not reach the patient and did not cause harm. Of the errors reported, 98.5% occurred in the prescribing phase of the medication process with 58.7% being due to calculation errors. Overall, 53 different medications were documented in error reports with the anti-infective agents being the most frequently cited. The majority of incidents indicated that the primary prescriber was contacted and the error was resolved before reaching the next phase of the medication process. Conclusion Medication errors reported by pharmacists occur most frequently in the prescribing phase of the medication process. Our data suggest that error reporting systems need to be specific to the population involved. Special attention should be paid to frequently used medications in the NICU as these were responsible for the greatest numbers of medication errors.