Background: Gross motor coordination (GMC) is a potential correlate of lifestyle behaviours and health outcomes in childhood and adolescence. Aims: The aim of this study was to examine how sex, age, biological maturation, overweight, stunting, and physical fitness are associated with GMC in children and adolescents from Peru, and to examine associations between geographical area of residence, school-level characteristics, and GMC. Subjects and methods: The sample included 7408 subjects, aged 6–14 years, from sea level, Amazon and high-altitude regions of Peru. A composite marker of total coordination was derived by the sum of scores from each test (GMCT). Overweight was identified using BMI, and biological maturation, physical fitness, and stunting were assessed. School characteristics were obtained via an objective audit. Results: Boys (β = 12.23 ± 0.90) and older children (β = 13.37 ± 0.64) had higher GMCT than girls and younger children, respectively. Overweight was associated with lower GMCT (β = −5.23 ± 0.80), whereas fitness was positively associated with GMCT (β = 6.30 ± 0.25). Biological maturation was not a predictor; however, stunting was negatively associated with GMCT (β = −3.71 ± 1.56). Subjects living in the Amazon had higher GMCT than those at sea level (β = 16.57 ± 4.73). Five of nine school-level predictors (number of students, playground area with obstacles, multi-sports roofed, frequency and duration of Physical Education classes) were significant predictors of GMCT. Conclusions: Child- and school-level variables were significantly associated with GMCT in this sample. These findings are important for the Peruvian community, especially school principals, councils and physical education teachers, helping them to define more efficient strategies and action plans to increase motor coordination in children.