While cardiac secondary prevention in primary care is established practice, little is known about its long-term cost effectiveness. This study examines the cost effectiveness of a secondary prevention intervention in primary care in the Republic of Ireland and Northern Ireland over 6 years. An economic evaluation, based on a cluster randomised controlled trial of 903 patients with heart disease, was conducted 4.5 years after the intervention ceased to be delivered. Patients originally randomised to the control received usual practice while those randomised to the intervention received a tailored care package over the 1.5-year delivery period. Data on healthcare costs and quality adjusted life expectancy were used to undertake incremental cost utility analysis. Multilevel regression was used to estimate mean cost effectiveness and uncertainty was examined using cost effectiveness acceptability curves. At 6 years, there was a divergence in the results across jurisdictions. While the probability of the intervention being cost effective in the Republic of Ireland was 0.434, 0.232, 0.180, 0.150, 0.115 and 0.098 at selected threshold values of €5000, €15,000, €20,000, €25,000, €35,000 and €45,000, respectively, all equivalent probabilities for Northern Ireland equalled 1.000. Our findings suggest that the intervention in its current format is likely to be more cost effective than usual general practice care in Northern Ireland, but this is not the case in the Republic of Ireland.