Stunting, defined as linear growth retardation, is a serious public health problem in developing countries. We aimed to (1) describe the prevalence of stunting in Peruvian youth living in three geographical regions, and to (2) determine height and physical fitness (PF) differences between stunted and normal-growth children across age and sex. We sampled 7918 subjects (7074 normal-growth and 844 stunted), aged 6–15 year, from sea-level, Amazon and high-altitude regions of Peru. PF was assessed with standardized tests, and stunting was computed following World Health Organization (WHO) standards. A two-factor analysis of variance (ANOVA) model was used. Results showed that stunting prevalence increased with age (from 6% at 6 year to 18.4% at 15 year in girls, and 9.3% at 6 year to 16.4% at 15 year in boys); was higher in boys (12.3%) than in girls (9.3%), and was higher in the Amazon region (25.3%), followed by high-altitude (24.3%) and sea-level (8.1%). Stunting had a negative overall impact on girls’ and boys’ statures. Further, the age-by-stunting interactions were statistically significant for both sexes, and significant differences in height varied to some degree across age. Stunted children performed worse in handgrip and standing long jump, but outperformed their normal-growth peers in shuttle-run (only boys), and in 12 min run. Further, significant differences in the age-by-stunting interaction occurred in all PF tests, varying to some degree across age. In conclusion, stunting significantly affects Peruvian youth’s PF levels, and this influence is sex-, age-and PF test-specific.