The scheme, which would see drivers pay according to which roads they use and when, would help reduce emissions, cut congestion and increase fairness, Reform Scotland said.
The organisation has produced a report on the idea, calling for the Scottish Government to launch a feasibility study on road pricing.
The scheme would require both vehicle excise duty (VED) - known as road or car tax - and fuel duty to be devolved to Holyrood in order for them to be abolished as the pay-as-you-drive system became live.
Reform Scotland said VED, while addressing carbon emissions through its grading structure, punishes those who drive infrequently by charging them exactly the same as those who drive on a regular basis.
It describes fuel duty as a "blunt instrument" which takes no account of which roads are being used or at what time.
Its report cites examples from other countries where similar schemes have been introduced, including Germany and Norway.
The Scottish Conservatives have already criticised the plans. The party's transport spokesman Alex Johnstone said: "While there may be some benefit for rural drivers, that in turn would result in commuters who absolutely need to use motorways and trunk roads paying through the nose.
"These people already pay a significant amount and charging them even more could also have a negative impact on the economy."