Generally, dental treatment should be discontinued for atypical odontalgia. However, the best timing for restarting dental treatment has not been sufficiently investigated. Here, we report a case of comorbidity of atypical odontalgia and odontogenic pain treated in collaboration with family dentists. <br>A 47-year-old female office worker complained of persistent dull and contact pain after root canal treatment in the upper right molar. Eight months ago, despite root canal retreatment of the upper right second molar and pulpectomy of the upper right first molar, the tooth pain persisted for several months. The pain continued to worsen with each dental procedure, so she was referred to our department. <br>Both of the teeth had spontaneous pain, and she felt pain when the teeth were only touched. Intraoral radiography and cone beam computed tomography did not reveal root fracture or perforation of either of the teeth. <br>She was diagnosed with comorbidity of atypical odontalgia and odontogenic pain. The symptom of atypical odontalgia was greater than that of odontogenic pain at the first visit, therefore she was prescribed amitriptyline 10mg/day, increasing to 30mg/day every week. Moreover, root canal treatment was stopped until the atypical odontalgia alleviated. <br>Spontaneous pain disappeared by 4 weeks, and occlusal pain was alleviated by 10 weeks. She was able to eat without pain at 18 weeks, and dental treatment was resumed at 24 weeks after the first visit. <br>Temporary exacerbation of odontogenic pain due to flare-up was observed when root canal treatment was restarted, but extraction of the upper right second molar and root canal treatment and prosthetic treatment of the upper right first molar were completed without exacerbation of atypical odontalgia. At 64 weeks, occlusal pain had completely disappeared, and finally at 73 weeks, medication was stopped after gradually decreasing the dose. <br>Atypical odontalgia and odontogenic pain often coexist. It is necessary to carefully determine whether atypical odontalgia or odontogenic pain is greater and to consider the priority of treatment. Accordingly, dental education is essential for this treatment. Research with a large number of cases on the timing of restarting dental treatment for comorbid atypical odontalgia and odontogenic pain is needed.