About 6,000 rocks are known in Britain to have ancient cup and ring carvings. More than 2,000 of the sites are found in Scotland.
Historic Environment Scotland (HES) has been awarded Â£807,000 by the Arts and Humanities Research Council towards the five-year project.
The database would include 2D and 3D models of some of the decorated stone.
The project will be launched next year and involve the University of Edinburgh and Glasgow School of Art.
The purpose and significance of rock art to prehistoric and more recent communities is poorly understood, HES said.
Archaeologists believe the markings may have been made for a number of reasons.
These include for rituals, as territorial markers or mapping the stars. They could even be the "doodlings" of bored, ancient shepherds.
New examples of rock art are still being found. The discovery of a previously unrecorded example was made in the Highlands in 2014.
Rebecca Bailey, who led the grant application for HES, said: "We are absolutely delighted to have secured our first very substantial research grant from the Arts and Humanities Research Council.
"The project will be a co-production between our expert staff, academic partners and community groups, in keeping with our vision that the historic environment is understood, shared and enjoyed by everyone.
"We look forward to the teams getting out into the field, making new discoveries, generating new knowledge, and sharing that on an international stage."
The project will be launched in early 2017. It will be led for HES by principal investigator Dr Tertia Barnett.
Co-investigators from the University of Edinburgh and Glasgow School of Art will also be involved and the project's partners include Archaeology Scotland, Kilmartin Museum and the North of Scotland Archaeology Society.
A digital database of Scotland's Neolithic and early Bronze Age rock art is to be created.