Complex interventions, such as parenting programs, are rarely evaluated from a public sector, multi-agency perspective. An exception is the Incredible Years (IY) Basic Parenting Program; which has a growing clinical and cost-effectiveness evidence base for preventing or reducing children’s conduct problems. The aim of this paper was to provide a micro-costing framework for use by future researchers, by micro-costing the 12-session IY Toddler Parenting Program from a public sector, multi-agency perspective. This micro-costing was undertaken as part of a community-based randomized controlled trial of the program in disadvantaged Flying Start areas in Wales, U.K. Program delivery costs were collected by group leader cost diaries. Training and supervision costs were recorded. Sensitivity analysis assessed the effects of a London cost weighting and group size. Costs were reported in 2008/2009 pounds sterling. Direct program initial set-up costs were £3305.73; recurrent delivery costs for the program based on eight parents attending a group were £752.63 per child, falling to £633.61 based on 10 parents. Under research contexts (with weekly supervision) delivery costs were £1509.28 per child based on eight parents, falling to £1238.94 per child based on 10 parents. When applying a London weighting, overall program costs increased in all contexts. Costs at a micro-level must be accurately calculated to conduct meaningful cost-effectiveness/cost-benefit analysis. A standardized framework for assessing costs is needed; this paper outlines a suggested framework. In prevention science it is important for decision makers to be aware of intervention costs in order to allocate scarce resources effectively.