This longitudinal cohort study investigated the incidence of postpartum depression (PPD) among mothers of infants cared for in two Neonatal Intensive Care Units (NICU) and factors related to PPD onset. 123 mothers were posted the Edinburgh Post-Natal Depression Scale (EPDS) and a questionnaire to record infant and maternal data at 1 month, and a repeat EPDS scale at 4 months post-discharge. PPD incidence was 15% at 1 month, 14% at 4 months, and varied by NICU (23% vs. 8%). Pre-pregnancy and/or antenatal depression was significantly associated with the incidence of PPD. Mothers who experienced PPD at 1 month had an almost eight fold risk of experiencing PPD at 4 months. Women who were not offered counselling during their infant’s stay on the NICU had a 60% increased risk for PPD onset. The findings highlight the need for routine pre-natal screening and targeted support for mothers with infants admitted to NICU.