Objectives. The immune response and the nature of the oral microflora in children with congenital cleft lip and palate (CLP) has its own characteristics, which are mainly determined by the anatomical and functional characteristics of the tissues in general and the insufficiency of immune system cells in particular. In recent years, the arsenal of physiotherapeutic treatment methods used in maxillofacial surgery has significantly expanded, which makes it possible to reduce the severity of clinical manifestations and reduce the incidence of disease complications. Purpose. To evaluate the effectiveness of magnetic laser therapy and herbal medicine in the form of lozenges on the microflora of the oral cavity in the postoperative period after uranoplasty in children with congenital cleft palate. Methodology. We examined 150 children aged 2–5 years with congenital cleft palate and 45 healthy children to clarify clinical and laboratory standards. Depending on the treatment, a group of 150 children with congenital cleft palate was divided into 4 subgroups. At the first stage of the study, all children underwent oral fluid collection and a swab from the oral cavity. Results. It was revealed that in children, when using lollipops with herbal medicine, the microflora significantly improved, as well as in comparison with groups in which MLT and MLT + herbal medicine were used in therapy. When the microflora of the oral cavity is normalized, reparative processes improve, and the postoperative wound regenerates in a short time without infection. Conclusions. Pain in the soft palate and pharynx during swallowing and eating persisted until the seventh day in children without the use of additional local therapy. When using the local therapy we proposed, the manifestations of inflammation in the area of the postoperative wound were less pronounced and disappeared on the third to fifth day.