Obesity is a worry because it is associated with a greater burden of disease, and it has been shown to be related to the health habits and physical condition of children and adolescents. Objective: To associate physical fitness, screen time, and sleep habits with the different categories of obesity in schoolchildren from the extreme south of Chile. Methods: 583 schoolchildren were included in this cross-sectional analysis. The screen time and sleep habits were measured with the Sleep Self-Report questionnaire, while the physical fitness was assessed with the Alpha Fitness test battery. The Body Mass Index/age (BMI/age) and the Waist-to-Height ratio (WtHr) were used to define adiposity using the following categories: healthy weight/low-risk waist-to-height ratio (H/LR), healthy weight/high-risk waist-to-height ratio (H/HR), overweight/low-risk waist to height ratio (O/LR), and overweight/high-risk waist to height ratio (O/HR). Results: A considerable number of schoolchildren (23.2%) presented sleep problems, while the mean screen time was 9.3 (95% CI: 8.4; 10.1) hours/day. Schoolchildren classified as H/HR showed better physical fitness than the O/HR group but worse physical fitness than the H/LR group. Conclusions: Significant differences were evidenced in the physical fitness between the adiposity categories, which could open future lines of research concerning the characterization of the healthy weight-obese adiposity categories in children.