In this study, we investigated the effect of several processing conditions on warpage in carbon-fibre/PEKK composites manufactured under non-isothermal conditions. A multi-level factorial design of experiments was employed to study the effect of process and design parameters on warpage. Analysis-of-variance was used to establish the significance of the main factors as contributors to warpage. The number of plies and consolidation pressure were the factors that contributed significantly to warpage. A regression model was used to predict the warpage of panels consolidated using aluminium tooling, giving a reasonably good prediction of less than 18% difference. A panel with variable thickness was also manufactured, based on the prior observations, pressure and lay-up configurations were successfully altered to reduce warpage. DSC results showed that the warpage of semi-crystalline PEKK composites consolidated under non-isothermal conditions is a result of a differential in shrinkage across the laminate, as the degree of crystallinity varied with temperature and consolidation pressure.