Background Digital health interventions (DHI) are associated with significant promise. In recent years, the need to assess the value of these healthcare technologies has motivated a debate regarding the suitability of existing economic evaluation methods in the context of DHI evaluation. Some have argued that robust economic evaluation methods may not be capable of capturing relevant DHI’s characteristics. Others consider that assessing the value of DHI might not be feasible. This protocol paper challenges that view. More specifically, it describes early Health Technology Assessments (HTA) methods to rigorously assess the value for money of a complex intervention including a digital decision support tool i.e., Improving uptake of Fracture Prevention drug treatments (iFraP) as a tracer intervention. iFraP is a complex intervention consisting of a computerised decision support tool, a clinician training package, and information resources to facilitate shared decision-making, increase informed medicine initiation and reduce levels of medicine discontinuation. iFraP’s development was motivated by a view that good quality shared decision-making conversations have the potential to improve levels of osteoporosis medicine uptake. Methods An early economic evaluation of the iFraP intervention was designed to identify, measure, and evaluate the costs and health benefits of iFraP compared to usual practice in Fracture Liaison Services (FLSs). A within-trial cost-effectiveness from the perspective of the National Health Service and Personal Social Service in England will be conducted using patient’s self-reported health related quality of life (HRQoL) and resource use from the iFraP randomised controlled trial. Microanalysis will be used to estimate iFraP’s intervention cost. Finally, Bayesian Value of Information analysis will allow us to estimate an upper bound for the potential health benefits gained from reducing uncertainty on the impact of the iFraP intervention to support uptake and adherence with osteoporosis medicines. Trial registration ISRCTN10606407 - https://doi.org/10.1186/ISRCTN10606407