This study aimed to evaluate the anxiety in paediatric patients during caries treatment, with Er:YAG laser and conventional rotary instruments, in combination with child-management technique Latent inhibition. A group of 126 6–12-year-old children with one or more untreated dentine carious lesions (ICDAS code 05) on the occlusal surface of a primary molar was divided into four equal treatment subgroups. A standardized caries treatment was performed with Erbium:YAG laser or conventional rotary instruments. In the intervention groups, Latent inhibition was used as an anxiety-management technique. During the procedure, objective and subjective stress parameters were recorded. Statistically significant reduction in mean heart rate and self-anxiety scores was seen in the combination of Er:YAG laser caries removal and child-management technique (p < 0.05). The use of laser cavity preparation in combination with the child-management technique Latent inhibition is the most effective method during the dental treatment of children. Er:YAG laser alone showed an advantage over the conventional method and equivalent effect to the combined use of conventional rotary instruments and behaviour management technique.