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Abstract Background Paediatric patients being treated for long-term physical health conditions (LTCs) have elevated mental health needs. However, mental health services in the community are difficult to access in the usual course of care for these patients. The Lucy Project – a self-referral drop-in access point—was a program to address this gap by enrolling patients for low-intensity psychological interventions during their treatment for LTCs. In this paper, we evaluate the cost-effectiveness of the Lucy Project. Methods Using a pre-post design, we evaluate the cost-effectiveness of the intervention by calculating the base-case incremental cost-effectiveness ratio (ICER) using outcomes data and expenses recorded by project staff. The target population was paediatric patients enrolled in the program with an average age of 9 years, treated over a time horizon of 6 months. Outcome data were collected via the Paediatric Quality of Life Inventory, which was converted to health utility scores using an instrument found in the literature. The QALYs were estimated using these health utility scores and the length of the intervention. We calculate a second, practical-case incremental cost-effectiveness ratio using streamlined costing figures with maximum capacity patient enrolment within a one-year time horizon, and capturing lessons learned post-trial. Results The base-case model showed an ICER of £21,220/Quality Adjusted Life Years (QALY) gained, while the practical model showed an ICER of £4,359/QALY gained. The practical model suggests the intervention garners significant gains in quality of life at an average cost of £309 per patient. Sensitivity analyses reveal use of staff time was the greatest determinant of the ICER, and the intervention is cost-effective 75% of the time in the base-case model, and 94% of the time in the practical-case model at a cost-effectiveness threshold of £20,000/QALY gained. Conclusions We find the base-case intervention improves patient outcomes and can be considered cost-effective according to the National Institute for Health and Care Excellence (NICE) threshold of £20,000—£30,000/QALY gained, and the practical-case intervention is roughly four times as cost-effective as the base-case. We recommend future studies incorporate a control group to corroborate the effect size of the intervention.