Background: Individuals with spinal muscular atrophy (SMA) are at risk for low bone mass (LBM). The objectives of this study were to compare bone mineral density (BMD) in ambulatory SMA and control participants, identify LBM, and evaluate the associations of function and physical activity (PA) with LBM. Methods: Thirty-five children and adults, nineteen SMA and sixteen healthy controls, participated. Dual-energy absorptiometry determined BMD, T-scores, and Z-scores. The six-minute walk test (6MWT) and Timed Up and Go (TUG) assessed function. The International Physical Activity Questionnaire Short Form (IPAQ-SF) evaluated PA. Results: Group comparisons and factors associated with BMD were analyzed. Area under the receiver operating characteristic (ROC) curve (AUC) assessed the ability to identify individuals with LBM. SMA participants had lower BMD (p < 0.001) and increased odds of having LBM relative to controls (OR = 16.7; 95%CI: 1.8–152.8; p = 0.004). Conclusions: Ten SMA and one control had LBM. Z-score was associated with 6MWT (r_s = 0.65; p < 0.001) and TUG (r_s = −0.61; p < 0.001). IPAQ-SF and Z-score were weakly associated (r_s = 0.36, p < 0.03). 6MWT (AUC: 0.80; 95% CI: 0.65–0.94; p = 0.006) and TUG (AUC: 0.85; 95% CI: 0.71–0.98; p = 0.002) identified individuals with LBM. Function, assessed by the 6MWT and TUG, is associated with BMD and shows promise for use in identifying individuals with LBM.