Objectives We aimed to compare the bone age (BA) estimation by a deep learning-based program and by a specialist in pediatrics of Korean medicine using the Tanner-Whitehouse 3 (TW3) technique for the cases of children who visited a Korean medicine hospital for growth, and to report the effect of Korean medicine treatment. Methods For three children who visited the Korean medicine hospital for growth, BA estimation by the deep learning program and by the specialist in pediatrics of Korean medicine using the TW3 technique was compared, and the time required for estimation was investigated. The change of height, BA, and predicted adult height (PAH) using deep learning program after Korean medicine treatment was observed. Results BA estimation of the left hand bone X-ray by the specialist using the TW3 technique showed a difference of -0.03 to +0.15 years from the estimation by the deep learning program. The mean estimation time was 5 minutes and 49 seconds per one for the specialist and 48 seconds for the deep learning program. During the treatment period, the height percentile and PAH estimated by deep learning program were increased after Korean medicine treatment compared to baseline while acceleration of BA was suppressed compared to chronological age. Conclusions BA estimation using the deep learning program and the TW3 technique showed a difference of less than 0.15 years, and in three cases of patients with growth as the chief complaint, Korean medicine treatment increased height percentile and PAH without accelerating BA maturation.