Thalassemic osteopathy (TOSP) has emerged as a topic of interest, as the optimized transfusion regimens and iron chelations has markedly improved the survival of the patients suffering from thalassemia major (TM) and increased the life expectancy. The aim of this prospective monocentric pilot study was to investigate the effects of a dietary supplement with vitamin K2 (50 mcg menaquinone-7) and vitamin D (5 mcg calcitriol) on the patients with TOSP. Twenty children (12 girls, 8 boys; age varied from 3 to 18 y) with β TM, who underwent regular blood transfusion and iron chelation therapy, were enrolled in this study and investigated at the initial, sixth, and 12th month of the treatment. We detected a significant improvement in the bone mineral density and Z-score at the lumbar spine area of the patients at the sixth and 12th month of the treatment, especially in the prepubertal group. We also found a decrease in the ratio of undercarboxylated osteocalcin to carboxylated osteocalcin, however, this was not found to be significant. Although the natural course of TOSP is worsening or at least stabilizing, our pilot study demonstrated that vitamin K2 and calcitriol combination clearly has a positive effect on the bone mineral density of the children with TM during a 1-year period. Supplementation of menaquinone-7 instead of drugs is an augmented physiological intake and seems a beneficial alternative for the treatment of TOSP. Further studies on a large number of participants are necessary to highlight the effect of vitamin K2 on TOSP.