Background: Children’s health is a current concern and data suggests that poor fundamental movement skills (FMS) could be associated with poor health, which may or may not be mediated by low physical activity level. However, tools to assess FMS have not been standardized, and could consequently lead to different associations between FMS and health indicators. Objective: The primary objective of this study was to evaluate the associations between FMS and health indicators using two different FMS measurement tools often used in Canada. Methods: A total of 145 children between the ages of 9 to 12 were recruited from schools, after school programs, and summer camps in 2016. FMS were evaluated using the Passport for Life (bound, plank, run, kick, throw) and the PLAYbasic (run, hop, throw, kick, and balance). The association between each test and an average score for each tool were tests with health indicators including anthropometric measures, grip strength, cardiorespiratory fitness, and percent body fat. Results: Participants were composed of 54.2% boys aged 10.4 ± 1.2 years with an average body mass index of 18.8 ± 3.8 kg/m2. The association between the average score of both tools was 0.77 (p < 0.01), body mass index was significantly associated with 67% of FMS elements using the Passport for Life (r ranging from −0.18 to −0.32; p < 0.05), and 60% of FMS using the PLAYbasic (r ranging from −0.15 to −0.30; p < 0.05). There were no significant differences between the associations of the health indicators with FMS and either FMS assessment tool (Passport for Life and PLAYbasic) (p = 0.05). Average score of FMS was significantly associated with all health indicators using both PLAYbasic and Passport for Life (all p < 0.05). Conclusions: Health indicators in children are associated with FMS regardless of whether the Passport for Life or the PLAYbasic was used as the assessment tool. It is worth investigating if interventions that improve FMS lead to improvements in these health indicators.