Background: Bone mass acquisition during growth is a major determinant of the risk of developing osteoporosis later in life. Body composition is an anthropometric determinant of bone mineral density (BMD) and significantly influences its development during childhood and adolescence. Objective: This study aimed to systematically examine the association between body composition and bone mineral density in children and adolescents. Methods: Observational studies addressing this association were identified from PubMed (MEDLINE), Embase, Scopus and the Cochrane Library (up to January 2021). The study populations consisted of healthy children and adolescents. The DerSimonian and Laird method was used to compute pooled estimates of effect size and the respective 95% confidence intervals for upper limbs, femoral neck (FN), lumbar spine (LS) and total body, respectively. Subgroup analyses were further performed based on age, sex and ethnicity. Results: Thirty-one published studies were eligible for inclusion in this systematic review and meta-analysis, including three longitudinal studies. The combined population from all the studies amounted to 21,393 (11,205 males and 10,188 females). The pooled estimates of the correlation coefficients for lean mass (LM) and BMD ranged from 0.53 to 0.74 (p < 0.050), and the pooled regression coefficients ranged from 0.23 to 0.79 for FN, LS and total body (p < 0.050). For fat mass (FM), the pooled correlation coefficients ranged from 0.10 to 0.50 (p < 0.050) and the pooled regression coefficient was only significant for FN BMD with a weak strength (pooled β = 0.07, p < 0.050). The pooled regression coefficients for body fat percentage (BF%) were between −0.54 and −0.04 (p < 0.050). The subgroup analysis revealed a stronger association in Asians than in Caucasians for LM and in males compared to females for BF% (p < 0.050). Conclusions: This systematic review and meta-analysis supports a positive association between LM and BMD. BF% appears to have a deleterious effect on bone acquisition in children and adolescents.