The aim of our study was to analyze the possible relationship between growing pains, vitamin D levels, and bone mineral status. We enrolled 33 children affected by growing pains. Their pain intensity was evaluated through a questionnaire using the Wong-Baker Faces Pain Rating Scale for pain assessment. Serum 25-hydroxyvitamin D (25-OH-D), parathyroid hormone (PTH), and alkaline phosphatase levels were measured as well. A quantitative ultrasound assessment (QUS) was also done, measuring both the amplitude-dependent speed of sound (AD-SOS) and the bone transmission time (BTT), correlating, respectively, with bone density and with cortical thickness. After 3 and 24 months of vitamin D supplementation, we re-evaluated pain intensity and laboratory results. After 24 months we re-assessed QUS parameters. At the beginning of the study the children reported a mean growing pain intensity of 7.5 ± 1.6 SD. The mean values of 25-OH-D and PTH levels were 15.7 ± 6.9 ng/ml and 57.3 ± 27.3 pg/ml, respectively. The AD-SOS Z score was -0.53 ± 1.19 SD, and the mean value of the BTT Z score was -0.72 ± 0.96 SD. After the first 3 months of vitamin D supplementation we observed an increase in 25-OH-D levels (34.1 ± 17.8, p < 0.001) and a reduction in both PTH levels (47.3 ± 30.6, p = 0.135) and pain intensity (2.7 ± 2.2, p < 0.001). After 24 months we observed a further significant reduction in the pain intensity (3.9 ± 3.4, p < 0.001) and in PTH levels (43.7 ± 28.5, p = 0.004) and an improvement in the QUS parameters, in particular in BTT Z scores (p = 0.014). Our study suggests an interesting relationship between growing pains, vitamin D levels and bone mineral status.