Leptin concentrations in breast milk can influence metabolic programming during the first months of life. Small for gestational age (SGA) newborns show a peculiar growth pattern after birth, which can lead to adulthood diseases. This study aims to assess an association between leptin concentration in mature breast milk and the infant anthropometric indicators of the SGA and the non-SGA groups, in addition, to comparing the hormone level between these groups. A longitudinal study was performed with mother-infant pairs. The maternal sociodemographic information was collected in the first 48 h postpartum. Breast milk was collected at one month postpartum and leptin concentrations were obtained by immunoassays. The infant anthropometric measurements were collected at three and six months postpartum and included weight, height (to body mass index-BMI calculated), triceps skinfold (TSF), and subscapular skinfold (SSF). The BMI for age (BMI/A), TSF, and SSF were calculated by Z-score indicators. Data from 67 mother-infant pairs (n = 16 SGA and n = 51 non-SGA) were analyzed. In univariate analyses, the breast milk of the SGA group had lower leptin concentrations than the non-SGA group (p = 0.006), however, after adjustment, there was no difference between groups (p = 0.181). In the SGA group, there was a significant association between leptin concentrations and lower SSF at six months in infants, after adjustment (p = 0.003). In the non-SGA group, the breast milk leptin was associated with lower BMI/A at three and six months in infants, after adjustment (p = 0.002 and p = 0.010, respectively). The association between breast milk leptin concentrations with SSF in the SGA group and BMI/A in the non-SGA group suggests that leptin may be a modulating factor in infant growth in the first months of life.