Background: Predicting the course and complications of perinatal depression through the identification of clinical subtypes has been previously undertaken using the Edinburgh Postnatal Depression Scale and has the potential to improve the precision of care and improve outcomes for women and their children. Methods: Edinburgh Postnatal Depression Scale scores were collected twice in pregnancy and twice in the postpartum in a sample of 360 women who met diagnostic criteria for perinatal depression using the Structured Clinical Interview for DSM disorder. These data were used to compare with previous, though conflicting, evidence from cross-sectional studies and extend this by undertaking longitudinal measurement invariance modelling to test the structural validity across the perinatal period. Latent profile and transition modelling was used to identify distinct subtypes of women and assess the utility of these subtypes and transition profiles to predict clinically meaningful outcomes. Results: Although our data supported one of the previously reported three-factor Edinburgh Postnatal Depression Scale structures used to compute subfactor totals for depressed mood, anxiety and anhedonia at both early pregnancy and 6 months postpartum, there was little value in using these Edinburgh Postnatal Depression Scale subfactor scores to identify subtypes predictive of clinically meaningful postpartum symptom subtypes, or of general health, pregnancy and neonatal outcomes. Conclusion: Our study does not support the use of the Edinburgh Postnatal Depression Scale to distinguish perinatal depressive subtypes for the purposes of predicting course and complications associated with perinatal depression. However, the results give guidance on alternative ways to study the value of personalised management in improved outcomes for women living with or at risk for perinatal depression.