Levying excise taxes on sugar-sweetened beverage (SSB) distributors, which are subsequently passed on to consumers, is a policy implemented to reduce the high prevalence of cardiometabolic disease and generate public health funding. Taxes are associated with lower SSB purchases and consumption, but it is unknown whether they are associated with weight-related outcomes in youth. To determine the association of SSB excise taxes with youth body mass index (BMI) trajectories. This cohort study was conducted from 2009 to 2020, including 6 years before tax implementation and 4 to 6 years after tax implementation. The California cities of Albany, Berkeley, Oakland, and San Francisco, which implemented SSB excise taxes, were compared against 40 demographically matched control cities in California. Participants included Kaiser Permanente members aged 2 to 19 years at cohort entry (baseline) with continuous residence in selected cities with at least 1 pretax and 1 posttax BMI recorded in their electronic health record. Data analysis was performed from January 2021 to May 2023. Implementation of SSB excise taxes. Centers for Disease Control and Prevention age-specific and sex-specific BMI percentiles and percentage of youth with overweight or obesity before tax implementation through 4 to 6 years after implementation were compared with control cities. Statistical analysis was conducted using the difference-in-differences (DID) method. A sensitivity analysis used the synthetic control method. A total of 44 771 youth (mean [SD] age at baseline, 6.4 [4.2] years; 22 337 female [49.9%]) resided in the cities with SSB taxes; 345 428 youth (mean [SD] age, 6.9 [4.2] years; 171 0168 female [49.5%]) resided in control cities. There was a -1.64-percentage point (95% CI, -3.10 to -0.17 percentage points) overall difference in the mean change of BMI percentile between exposure and control cities after SSB tax implementation. There was no significant overall difference in the percentage of youth with overweight or obesity or youth with obesity compared with control cities. All DID estimates were significant for youth residing in exposure cities in terms of BMI percentile (age 2-5 years in 2017, -2.06 percentage points [95% CI, -4.04 to -0.09 percentage points]; age 6-11 years in 2017, -2.79 percentage points [95% CI, -4.29 to -1.30 percentage points]), percentages of youth with overweight or obesity (age 2-5 years, -5.46 percentage points [95% CI, -8.47 to -2.44 percentage points]; age 6-11 years, -4.23 percentage points [95% CI, -6.90 to -1.57 percentage points]), and percentages of youth with obesity (age 2-5 years; -1.87 percentage points [95% CI, -3.36 to -0.38 percentage points]; age 6-11 years, -1.85 percentage points [95% CI, -3.46 to -0.24 percentage points]). Compared with control cities, changes in mean BMI percentiles were significant for male (-1.98 percentage points; 95% CI, -3.48 to -0.48 percentage points), Asian (-1.63 percentage points; 95% CI, -3.10 to -0.16 percentage points), and White (-2.58 percentage points; 95% CI, -4.11 to -1.10 percentage points) youth. Compared with control cities, White youth in exposure cities had improvements in the percentage with overweight or obesity (-3.73 percentage points; 95% CI, -6.11 to -1.35 percentage points) and the percentage with obesity (-2.78 percentage points; 95% CI, -4.18 to -1.37 percentage points). In this cohort study, SSB excise taxes were associated with lower BMI percentile among youth. Policymakers should consider implementing SSB excise taxes to prevent or reduce youth overweight and obesity and, ultimately, chronic disease, particularly among children younger than 12 years.