Background: Early discharge from the hospital against medical advice poses a significant threat to the health of patients, particularly neonates, who are a vulnerable population. Objectives: This study aimed to determine the frequency of neonatal discharge with personal consent and identify the most influential factors. Methods: This retrospective cross-sectional study was conducted at Alzahra Hospital in Rasht from 2020 to 2021. Using a census method, information on all infants discharged against medical advice was extracted from the hospital's clinical records available in the information system. Data on the reason for neonatal hospitalization and discharge against medical advice, neonatal age, weight, maternal education, and insurance status were recorded. Results: Among 2327 neonates, 581 (24.96%) were discharged from the hospital against medical advice. The primary cause of early discharge was related to family problems (64.4%), followed by dissatisfaction with the hospital and treatment process (15.3%), prolonged hospitalization (11%), and financial problems (9.3%). A significant association was found between neonatal age, weight, type of delivery, maternal education, insurance status, and the reason for hospitalization with the reason for discharge against medical advice (all P < 0.001). Conclusions: The rate of discharge against medical advice in this study was notably higher compared to other studies, possibly due to the timing of the study coinciding with the peak of COVID-19 and the different reasons for hospitalization, such as icterus versus sepsis. Family problems were identified as the main cause of discharge against medical advice, while financial problems were the least common. Therefore, practical and preventive solutions should be provided to families whenever possible.