Patient engagement in treatment decision-making is essential to improve the health-related quality of life (HRQoL) of patients affected by chronic diseases. However, research on how decision-making patterns influence HRQoL is limited. This study investigated the paths linking patient experience in decision-making to HRQoL through healthcare accessibility and physical activity among a representative sample of adults with chronic diseases. Using a cross-sectional design, the data of 4,071 individuals with chronic diseases from the 2015 Korea National Health and Nutrition Examination Survey were analyzed. We used R to account for the complex survey design and weights and conducted structural equation modeling. The EuroQoL 5 Dimensions were used to assess HRQoL. About half of the participants reported that providers always offered sufficient encounter time (48.8%), used lay terms (60.4%), provided opportunities for questions (57.8%), and reflected patient opinions on treatment plans (57.8%). Healthcare accessibility completely mediated the association between patient experience in decision-making and HRQoL, whereas decision-making experiences directly affected HRQoL, not via physical activity. Clinicians should provide solid and tailored advice that entails benefits and detriments to achieve evidence-based decision-making. Programs to enhance access to after-hour healthcare should be considered to improve patients' HRQoL.