Coffee consumption in the pediatric population is not popular. The potential influence of caffeine on children’s health remains controversial. Unfortunately, the main sources of caffeine in children are soda and energy drinks that are devoid of precious ingredients of coffee like riboflavin, niacin, magnesium, potassium, and various phenolic compounds, or antioxidants. Taking into account that caffeine may pass through the blood–placental barrier, the influence of this substance on human health starts in utero. There are some studies that showed the correlation between coffee intake by pregnant women and intrauterine growth retardation (IUGR), subfertility, spontaneous abortion, as well as childhood overweight, cognitive impairments, or autism spectrum disorder-related (ASD-related) behaviors. Methylxanthines, including caffeine, are respiratory stimulants with a therapeutic effect that have been used in preterm infants for decades. In the literature, there is some evidence of caffeine influence on the child’s health status, including growth and bone metabolism, obesity occurrence, or nervous system functions. Moreover, it was shown that caffeine acted as a colonic stimulant in pediatric patients. In this review, we will focus on the health effects of coffee on the child’s health status in various aspects and on the subsequent parts of life.