Background: While many cancer survivors experience persistent impairments in health-related quality of life (HRQoL) for extended periods of time, others recover soon after treatment. The aim of this research is to assess changes in health-related quality of life in endometrial and ovarian cancer survivors during two years post initial treatment, and to assess clinical and sociodemographic characteristics associated with those changes. Methods: This prospective population-based cohort study includes longitudinal data of endometrial (N ¼ 221) and ovarian (N ¼ 174) cancer survivors diagnosed between 2011 and 2014. The EORTC QLQ-C30 functioning scales were used to assess HRQoL after initial treatment and after 6, 12 and 24 months. Clinical (stage, treatment and comorbidities) and sociodemographic (age, marital status and socioeconomic status) characteristics were obtained from the Netherlands Cancer Registry and through self-administered questionnaires. Linear mixed models were used to assess changes in HRQoL over time and characteristics associated with these changes. Results: Among both endometrial and ovarian cancer patients, HRQoL improved within the first 6 months after initial treatment. Changes in HRQoL were mainly associated with clinical characteristics including comorbidities, treatment and tumor stage, and to a lesser extent with sociodemographic characteristics such as socioeconomic status. However, these associations varied per tumor type. Endometrial cancer survivors, who received radiotherapy and had no comorbidities, reported greater improvements in some HRQoL scales over time. Ovarian cancer patients who received chemotherapy and with advanced tumor stages reported poorer functioning during treatment. Most functioning domains (global health, physical and role functioning) recovered to levels of patients without chemotherapy or with early-stage disease after 12 months, but cognitive and social functioning remained impaired. Conclusion: Some subgroups of patients, including those with multiple comorbidities, with an advanced tumor stage and who received chemotherapy, may be in need of additional support as they are less likely to show improvements in HRQoL over time.