Post-natal growth influences short- and long-term preterm infant outcomes. Different growth charts, such as the Fenton Growth Chart (FGC) and INTERGROWTH-21st Preterm Post-natal Growth Standards (IG-PPGS), describe different growth curves and targets. This study compares FGC- and IG-PPGS-derived weight-for-postmenstrual age z-score (WZ) up to 50 weeks postmenstrual age (PMA50) for predicting 1-year anthropometry in 321 South African preterm infants. The change in WZ from birth to PMA50 (ΔWZ, calculated using FGC and IG-PPGS) was correlated to age-corrected 1-year anthropometric z-scores for weight-for-age (WAZ), length-for-age (LAZ), weight-for-length (WLZ) and BMI-for-age (BMIZ), and categorically compared with rates of underweight (WAZ < -2), stunting (LAZ < -2), wasting (WLZ < -2) and overweight (BMIZ > + 2). Multivariable analyses explored the effects of other early-life exposures on malnutrition risk. At PMA50, mean WZ was significantly higher on IG-PPGS (-0.56 ± 1.52) than FGC (-0.90 ± 1.52; p < 0.001), but ΔWZ was similar (IG-PPGS -0.26 ± 1.23, FGC -0.11 ± 1.14; p = 0.153). Statistically significant ΔWZ differences emerged among small-for-gestational age infants (FGC -0.38 ± 1.22 vs. IG-PPGS -0.01 ± 1.30; p < 0.001) and appropriate-for-gestational age infants (FGC + 0.02 ± 1.08, IG-PPGS -0.39 ± 1.18; p < 0.001). Correlation coefficients of ΔWZ with WAZ, LAZ, WLZ and BMIZ were low (r < 0.45), though higher for FGC than IG-PPGS. Compared with IG-PPGS, ΔWZ < -1 on FGC predicted larger percentages of underweight (42% vs. 36%) and wasting (43% vs. 39%) and equal percentages of stunting (33%), while ΔWZ > + 1 predicted larger percentages overweight (57% vs. 38%). Both charts performed similarly in multivariable analysis. Differences between FGC and IG-PPGS are less apparent when considering ΔWZ, highlighting the importance of assessing growth as change over time, irrespective of growth chart.