Polychlorinated naphthalenes (PCNs) are dioxin-like compounds that have been reported to be present in a wide variety of foodstuffs. Milk-based infant and toddler formula sometimes plays an important role in the diet of young children and could potentially cause adverse effects if contaminated with PCNs. This study investigated the concentrations of PCNs in commercial milk-based formula produced in different countries and sold on the Chinese market for three age groups: 0–6, 6–12 and 12–36 months. The total concentrations of PCNs in 72 samples from different countries of formula based on cow milk ranged from 7.8 to 30.3 pg/g whole weight (ww). Although the PCN concentrations in formula produced in Asia, Europe and South Pacific varied, all had comparable toxic equivalent (TEQ) values. Tri-CNs were the predominant PCN homologue in all samples. No significant differences in the concentrations of PCNs were found between samples of formula for each of the three age groups. The mean TEQ for PCNs in goat milk formula samples (0.0031 pg TEQ/g ww) was higher than the value for cow milk formula (0.0009 pg TEQ/g ww) produced in China, and the proportion of higher chlorinated PCNs in goat milk formula was also higher. Based on dry weight, the mean concentration of PCNs in the raw cow milk (119 pg/g dry weight (dw)) used to produce infant and toddler formula was higher than that in the actual formula (24.2 pg/g dw), and the PCN profiles also varied between the raw milk and formula. A risk assessment indicated that, in China, consuming formula poses a lower risk to infants and toddlers from based on exposure to PCNs compared with consuming breast milk.