Background Sugar-containing ultra-processed (SUP) foods and beverages consumption has increased globally in recent years and contributes to the rising global trends of obesity and diet-related chronic non-communicable diseases. However, there are limited longitudinal studies of SUP foods and beverages intake and weight gain in children. Objectives To examine associations between intake of sugar-sweetened beverages (SSB) and SUP foods and changes in body mass index during early childhood. Methods Multistage sampling was used to select a nationally representative sample of Uruguayan children living in urban areas from the 2012–2013 Continuous Household Survey. The sample for this analysis included all children aged 0–3 years 11 months with dietary data in 2013–2014 (wave 1; n = 2611) and in 2015–2016 (wave 2; n = 2383). Multilevel regression modelling tested the association between children's consumption of SSB and SUP foods and change in BMI z-score (BMIz). Results In multivariable-adjusted models, intake of SSB and SUP foods (in combination but not individually) in both waves was positively associated with change in BMIz over 2 years β coefficient: 0.13 (95% confidence interval [CI]: 0.02, 0.23). BMIz decreased among non-consumers (β: −0.12, 95% CI: −0.24, −0.00, p = 0.048). Associations were significant for SUP foods but not SSB foods individually. Children consuming ≥2 SSB and SUP foods (vs. <2) at baseline had increased BMIz (p for trend = 0.02). Conclusion Early and current intake of SSB and SUP foods and beverages was associated with increases in BMIz in children over 2 years.