This study investigated alterations in the foveal microvasculature following the administration of 0.125% atropine in myopic children. In this prospective study, 63 eyes from 36 individuals aged 5-18 years with myopia were administered 0.125% atropine for myopia control. After administration, foveal microvascular parameters such as the area and perimeter of the foveal avascular zone (FAZ), the acircularity index (AI) of FAZ, and foveal vessel density were evaluated longitudinally. The effect of atropine on foveal microvasculature was analyzed using a linear mixed model. One month after atropine application, the area and perimeter of FAZ significantly decreased (p = 0.014 and 0.041). A significant decrease in vessel density within the 300-µm wide annulus around FAZ and an increase in the AI of the FAZ were observed in the initial 3-month period (p = 0.035 and p = 0.047, respectively). However, changes in the FAZ area, perimeter, AI and foveal vessel density throughout the follow-up were not significant. These findings suggest that 0.125% atropine may induce transient changes in FAZ size and foveal vessel density, but its overall safety in managing myopia is supported by the stability of foveal parameters over time.