Background: Few studies have investigated unspecified or idiopathic pain associated with COIVD-19. This study aimed to provide the incidence rates of unspecified pain and idiopathic pain in patients with COVID-19 for 90 days after COVID-19 diagnosis. Methods: A propensity score matched cohort was used, including all patients with COVID-19 in South Korea, and analyzed their electronic medical records. The control group consisted of those who had not had tests for COVID-19 at all. Unspecified pain diagnoses consisted of diagnoses related to pain included in the ICD-10 Chapter XVIII. Idiopathic pain disorders included fibromyalgia, temporomandibular joint disorders, headaches, chronic prostatitis, complex regional pain syndrome, atypical facial pain, irritable bowel syndrome, and interstitial cystitis. Results: After matching, the number of participants in each group was 7,911. For most unspecified pain, the incidences were higher in the COVID-19 group (11.7%;95% confidence interval [CI], 11.0–12.5) than in the control group (6.5%; 95% CI, 6.0–7.1). For idiopathic pain, only the headaches had a significantly higher in-cidence in the COVID-19 group (6.6%; 95% CI, 6.1–7.2) than in the control group (3.7%; 95% CI, 3.3–4.1). However, using a different control group that included only patients who visited a hospital at least once for any reasons, the incidences of most unspecified and idiopathic pain were higher in the control group than in the COVID-19 group. Conclusions Patients with COVID-19 might be at a higher risk of experiencing unspecified pain in the acute phase or after recovery compared with individuals who had not had tests for COVID-19.