This document provides a decision-making framework for implementation of mass treatment interventions, active case-finding campaigns and population-based surveys for neglected tropical diseases in the context of the COVID-19 pandemic. A two-step approach is proposed: a risk–benefit assessment, to decide if the planned activity should proceed; and an examination of a list of precautionary measures that should be applied with the aim of decreasing the risk of transmission of COVID-19 associated with the activity, and strengthening the capacity of the health system to manage any residual risk. This guidance note is intended to health authorities, NTD programme managers and their supporting partners.