The Food & Drug Administration (FDA) convened a workshop to discuss clinical trial design challenges and considerations related to the treatment of non-tuberculous mycobacterial pulmonary disease (NTM-PD), to include topics such as clinical trial endpoints, duration, and populations. Here the clinicians participating in the meeting provide their interpretation of the discussion, which included FDA and industry representatives. The treatment of NTM-PD typically includes multiple antibiotics for a prolonged period, can be difficult to tolerate, and there is great need for new treatment options. Most individuals have a microbiologic response to therapy, but currently there is a lack of data correlating decreasing bacillary load with patient-reported outcomes or measured functional improvement. Accordingly, trial designs for new therapeutics should incorporate both microbiologic and clinical outcome measures and select appropriate study candidates with capacity for measurable change of such outcome measures. The need for shorter study designs, early primary endpoints, and placebo control arms was highlighted during the workshop.