Background: Phyto therapy or herbal therapy is one of the major branches of CAM that has been common in many countries, including Iran, since a long time ago. It was used as a rich source of pharmaceutical ingredients in various diseases. This study aimed to investigate the use of herbal medicines in the newborns referring to neonatal emergency department. Methods: The present descriptive, cross-sectional study was conducted on 30 parents of the infants admitted to the neonatal emergency department. A questionnaire was used to collect the information about the newborns and their parents, using herbal medicines, type of herbal drugs used for the infants, existence or absence of complications, and the person recommending the use of herbal medicines. The data were analyzed using the SPSS statistical software and descriptive statistics. Results: The results showed that 24 parents (80%) had used or were using herbal therapies for their infants. These drugs included Jujube, Purgative manna, Manna of hedysarum, Fumitory, Chicory, Castor oil, Ghee butter, Torbak lips, Frankincense and Rock sugar, Sisymbrium irio, Plantago major, Violet flower, Citrus limetta, Thymus vulgaris, Adiantum capillus-veneris, Cassia, and Garden morus and the highest rate was related to Jujube, Purgative manna, and Manna of hedysarum. Besides, 70% and 30% of these drugs were recommended by grandmothers and medicinal herbs sellers, respectively. According to the results, 95.2% of the parents believed that these drugs had no complications, while 4.8% had observed toxicity. In addition, 83.3% of the parents had also used these drugs for their previous children and reported their positive impact. Conclusions: Considering the fact that 80% of the parents had used herbal medicines for their infants, herbal medicines are recommended to be used under a physician's supervision and recorded in the patients' medical records.