Few existing efforts to predict childhood obesity have included risk factors across the prenatal and early infancy periods, despite evidence that the first 1000 days is critical for obesity prevention. In this study, we employed machine learning techniques to understand the influence of factors in the first 1000 days on body mass index (BMI) values during childhood. We used LASSO regression to identify 13 features in addition to historical weight, height, and BMI that were relevant to childhood obesity. We then developed prediction models based on support vector regression with fivefold cross validation, estimating BMI for three time periods: 30–36 (N = 4204), 36–42 (N = 4130), and 42–48 (N = 2880) months. Our models were developed using 80% of the patients from each period. When tested on the remaining 20% of the patients, the models predicted children’s BMI with high accuracy (mean average error [standard deviation] = 0.96[0.02] at 30–36 months, 0.98 [0.03] at 36–42 months, and 1.00 [0.02] at 42–48 months) and can be used to support clinical and public health efforts focused on obesity prevention in early life.