Incidence and neonatal risk factors for short stature in preterm children born small for gestational age (SGA) have not been fully investigated in Japan. In this prospective study, infants born ≤32 weeks' gestational age (GA) from 2004-2015 were enrolled and followed for 3 years. Incidence of short children born SGA and short stature treated with growth hormone (GH) were investigated. Neonatal risk factors were analysed using univariate and multivariate analyses. GA cut-off value was determined using receiver operating characteristic (ROC) curve analyses. Of 604 infants born ≤32 weeks' GA, 76 (13%) were SGA at birth. Twenty-seven infants (36%) developed short stature at age 2 and 14 infants (19%) received GH treatment at age 3. GA, birthweight, birth length, birth head circumference, and chronic lung disease at 36 weeks' corrected GA were determined as risk factors by univariate analyses (p < 0.01). Multivariate analyses only revealed low GA as an independent risk factor. ROC curve analysis determined a cut-off value of 24 weeks' GA. Nineteen percent of preterm SGA infants ≤32 weeks' GA developed short stature treated with GH. A low GA at birth could be an early detection marker for short stature that requires GH treatment in preterm infants born SGA.