Sugar-containing beverages (SCBs) are a major source of sugar intake in children. Early life intake of SCBs may be a strong predictor of SCB intake later in life. The primary objective of this study was to evaluate if SCB intake (defined as 100% fruit juice, soda, and sweetened drinks) in early childhood (≤2.5 years of age) was associated with SCB intake in later childhood (5–9 years of age). A prospective cohort study was conducted using data from the TARGet Kids! primary care practice network (n = 999). Typical daily SCB intake was measured by parent-completed questionnaires. Odds ratios (OR) and 95% confidence intervals (CI) were estimated using logistic regression. A total of 43% of children consumed ≥0.5 cups/day of SCBs at ≤2.5 years and this increased to 64% by 5–9 years. Daily SCB intake, compared to no daily intake, at ≤2.5 years was significantly associated with SCB intake at 5–9 years (adjusted OR: 4.03; 95% CI: 2.92–5.55) and this association was much stronger for soda/sweetened drinks (adjusted OR: 12.83; 95% CI: 4.98, 33.0) than 100% fruit juice (OR: 3.61; 95% CI: 2.63–4.95). Other early life risk factors for SCB intake at 5–9 years were presence of older siblings, low household income, and shorter breastfeeding duration. Daily intake of SCBs in early childhood was strongly associated with greater SCB intake in later childhood. Early life may be an important period to target for population prevention strategies.