The development and launch of the John Muir Way was funded by NatureScot (formerly Scottish Natural Heritage), Sustrans, Sportscotland, Forestry Commission, Europe (SRDP), Creative Scotland, local authorities and the Green Action Trust (formerly the Central Scotland Green Network Trust). Subsequent management and development has been funded by the Green Action Trust, NatureScot and Scottish Enterprise.

Promotion of the route and related business development is currently funded by the Scottish Government and the European Community through the LEADER 2014–2020 Programme, with additional funding from Local Authorities along the John Muir Way, Scottish Enterprise and the Green Action Trust. In addition, there are work programmes under way with funding from VisitScotland and Scotland Loves Local, including an artwork study for the Helensburgh terminus of the way.