Background: We share our experience of managing multiple endocrine neoplasia (MEN) 2A syndrome in pregnancy during the COVID-19 pandemic. The case highlights the various challenges we faced in patient management, surgical intervention, and follow-up during the lockdown along with how these challenges were overcome through multidisciplinary teamwork, teleconsultation services, and shared decision-making with the patient which led us to a successful outcome in a difficult clinical scenario, in such challenging times. Case presentation: Our patient was a 20-year-old lady diagnosed with MEN 2 syndrome which underwent an adrenalectomy for pheochromocytoma following which she became pregnant while awaiting her surgery for MTC. Subsequently, India entered a nationwide lockdown owing to the global COVID-19 pandemic and thyroidectomy had to be done at 24 weeks period of gestation (POG). The patient subsequently delivered at 37 weeks with an uneventful peripartum period. Conclusion: The overall rarity of this syndrome along with the scant literature available on its management in pregnancy posed significant challenges for the treating team. This was further compounded by the COVID-19 pandemic and diversion of healthcare resources for managing those afflicted which made it very difficult to provide individualized care, which is mandated in such cases. To the best of our knowledge, ours is the first case of pregnancy in a patient with MEN-2A syndrome to be successfully managed and reported.