Purpose Little is known about the relationship between apelin and serotonin in emotion regulation. This study aimed to examine children’s emotional regulation skills and salivary apelin and serotonin levels. Methods This is a cross-sectional study performed in Türkiye. The research was completed with the participation of 146 children, 8–10 years old, from the general population. Emotion Regulation Skills Scale for Children (CERS) was used to assess children’s levels of emotion regulation skills. Apelin and serotonin levels were examined by ELISA technique in saliva samples obtained from children. Results A statistically significant correlation was found between the mean total score of the CERS and the mean apelin and serotonin levels (p ˂ .01). We found that females had higher emotion regulation skills compared to males, older higher than younger ones (p ˂ .01). The regression analysis results show that age and gender together explain 50.5% of the variance in CERS scores, while apelin and serotonin together explain 35.8% of the variance. When all four variables (age, gender, apelin, and serotonin) are included in the model, they explain 51.3% of the variance in CERS scores. Conclusion Older age and female gender explained most of emotion regulations skills. Key points It was determined that the average salivary apelin and serotonin levels increased with increased age, and with increased age ERS also increased. More research is needed as this is the first time that the relationship between emotion regulation skills and serotonin and apelin levels has been examined.