Thrombocytopenia has been closely associated with small-for-gestational-age neonates (SGA; birthweight less than tenth percentile) admitted to the special care nursery or neonatal ICU. It is unclear if 'well' SGA neonates experience the same incidence of thrombocytopenia in the SGA population as compared to sick neonates. We conducted a retrospective cohort study from a health network in Melbourne, Australia, between 2012 and 2015 to identify SGA neonates (≥ 35 weeks' gestation at birth) that were otherwise well. Neonates with at least one platelet count within 7 days of life were matched to appropriate-for-gestational-age (AGA) neonates from the same birth centre, with the same sex, and closest gestational age and birth date, who were also considered otherwise well. 16.7% of matched neonates had thrombocytopenia (303/1814) and of these, a larger proportion of SGA neonates were thrombocytopenic, 21.7% (197/907), than AGA neonates, 11.7% (106/907, P < 0.01). The incidence of thrombocytopenia was greater in the SGA cohort regardless of admission destination (special care nursery/neonatal ICU 26.8 vs. 13.9%, P < 0.01; Postnatal Ward 16.5 vs. 9.4%, P < 0.01). Thrombocytopenia is more prevalent amongst constitutionally well SGA neonates than AGA neonates. SGA alone increases the risk of thrombocytopenia.