We describe our experience conducting a prospective observational cohort study on the management of small, low risk papillary thyroid cancer during the COVID-19 pandemic. Our study participants are given the choice of active surveillance (AS) or surgery, and those in the AS arm are followed at the study center, whereas surgical patients undergo usual care. During the pandemic we have transitioned from in-person research patient visits to largely virtual care of patients under AS. As of 30 October 2020, we had enrolled 181 patients enrolled in our study (including 25 during the pandemic), of which 92.3% (167/181) consented to telephone communication and 79.0% (143/181) consented to secure videoconferencing communication. Prior to the pandemic, 74.5% (117/157) of our patients chose AS over surgery, whereas during the pandemic, 96.0% (24/25) chose AS. Of the 133 study patients who were under AS within the timeframe from 12 March 2020, to 30 October 2020, the percentage of patients who missed appointments was 8.3% (11/133, for neck ultrasound and physician visits, respectively) and delayed appointments was 23.3% (31/133). This preliminary data suggests that prospective observational research on AS of thyroid cancer can safely continue during the pandemic.