Background Examples of precision medicine are complex interventions featuring both testing and treatment components. Because of this complexity, there are often barriers to the introduction of such interventions. Few economic evaluations attempt to determine the impact of these barriers on the cost-effectiveness of the intervention. This study presents a case study economic evaluation that illustrates how the value of implementation methods may be used to quantify the impact of capacity constraints in a decision-analytic model. Methods A baseline decision-analytic model-based economic evaluation of ALK mutation testing was reproduced from a published technology appraisal. Three constraints (commissioning awareness, localization of testing, and pathology laboratory capacity) were identified using qualitative interviews, parameterized, and incorporated into the model. Value of implementation methods were used alongside incremental cost-effectiveness ratios (ICERs) to quantify the impact on the cost-effectiveness and net monetary benefit (NMB) of each capacity constraint and from the 3 constraints combined. Results Each of the 3 capacity constraints resulted in a loss of NMB ranging from £7773 (0.1% of the total) per year for localized testing to £4,907,893 (77%) for a lack of awareness about commissioning ALK testing. When combined, the constraints resulted in a loss of NMB of £5,289,414 (83%). The localization and limited pathology capacity constraints slightly increased the ICER, but the lack of commissioning awareness constraint did not change the ICER. Conclusions Capacity constraints may have a significant impact on the NMB produced by examples of precision medicine. Value of implementation methods can be used to quantify the impact of such constraints by combining the impact of the constraints on the cost-effectiveness of the intervention with the impact on the number of patients receiving the intervention. Highlights While capacity constraints may prevent the use of precision medicine in clinical practice, economic evaluations rarely account for the impact of such barriers. This study demonstrates how constraints can be identified using qualitative methods and subsequently incorporated into decision-analytic models using quantitative value of implementation methods. In addition, this article demonstrates how value of implementation methods can be used to account for the impact of capacity constraints on the costs and benefits of an intervention as well as the number of patients receiving the intervention. In the case study presented herein, a capacity constraint reducing patient access to an example of precision medicine caused the biggest loss of net monetary benefit. Health economists should consider moving beyond incremental cost-effectiveness ratios to measures of total net monetary benefit to fully capture the impact of implementing precision medicine.