The rapid proliferation of healthcare service applications (apps) makes it challenging for consumers to determine the best one for their needs, prompting the Korean government to introduce an accreditation program to verify app safety. This study aims to identify the factors influencing the choice of healthcare service apps among physicians, patients with chronic diseases, and healthy individuals. We conducted a choice-based conjoint analysis with six factors (number of studies on effectiveness, frequency of information delivery, cybersecurity and data safety, user satisfaction, accreditation, and costs). 1,093 participants (407 healthy individuals, 589 patients, and 97 physicians) participated in the online survey. Across all groups, cybersecurity and data safety were the most important preference factors (healthy individuals: β = 2.127, 95% CI 2.096-2.338, patients: β = 1.569, 95% CI 1.481-1.658, physicians: β = 1.111, 95% CI 0.908-1.314). All groups were willing to pay more approximately $12 for high cybersecurity and data safety compared to low.