The objective of this study was to estimate change over time in health-related quality of life (HRQoL) of children with spinal muscular atrophy (SMA) in Sweden. Children with SMA were identified via the National Patient Register by the National Board of Health and Welfare in Sweden. Patient HRQoL was caregiver proxy-assessed using the Pediatric Quality of Life Inventory 4.0 Generic Core Scales at baseline, as well as at 6, 12, and 18 months of follow-up. Results were stratified by SMA type. Mothers and fathers to 27 children with SMA (mean patient age: 9.17 years; 59% female) participated in the study. All patients received disease-modifying therapy. At baseline, across SMA types, the mean total score was estimated at between 52.68 and 59.19, Physical Functioning score at between 26.39 and 40.34, Emotional Functioning score at between 66.82 and 68.57, Social Functioning score at between 55.00 and 70.45, and School Functioning score at between 70.45 and 78.33. The mean annual total score change was estimated at −2.03 for SMA type I, 4.11 for SMA type II, and 1.12 for SMA type III. In conclusion, we show that SMA has a detrimental impact on HRQoL that extends above and beyond somatic disability. Children with SMA type II experienced a dramatic increase in HRQoL over time, predominantly related to improvement in physical and social functioning. Our data helps quantify the patient burden of disease and adds to the rapidly expanding body of evidence of the effectiveness of recently approved disease-modifying therapies for SMA.