Purpose Pelvic exenteration offers significant survival benefits for patient with locally advanced rectal cancer however, postoperative morbidity remains high. The aim of this study was to determine the impact of postoperative morbidity on postoperative quality of life (QoL) trajectories following pelvic exenteration. Methods This prospective cohort study included patients who underwent pelvic exenteration between 2008 and 2023 at Royal Prince Alfred Hospital, Sydney. QoL measures were collected at baseline, 6, 12, 18, 24, 36, 48, and 60 months using the short-form 36 (SF-36v2) survey. Postoperative outcomes included length of stay (LOS), ICU stay, postoperative complications and mortality. Mixed-effects analyses were used to determine differences QoL trajectories based on postoperative outcomes. Results This study consisted of 674 patients, with median age of 61 years. Recurrent rectal cancer was the most common indication for surgery (36.1%). 47.2% of patients underwent partial, and 52.8% underwent complete pelvic exenteration. 48.9% of the cohort underwent sacrectomy. Shorter LOS, ICU stay and fewer (or no postoperative complications) were associated with better physical QoL outcomes at all time points. Conversely, postoperative morbidity did not significantly impact mental QoL outcome. Furthermore, there was a longitudinal improvement in mental QoL outcomes, independent of postoperative morbidity. Conclusion Higher morbidity following pelvic exenteration were associated with poorer health related quality of life trajectories. Interventions aimed at mitigating postoperative morbidity may enhance long-term QoL outcomes following pelvic exenteration.