Regional boards will see a £248 million uplift for 2014/15, bringing their total funding pot to £9.33 billion, representing an overall 3.1% increase, or 1% above inflation.
NHS Orkney, Lothian and Grampian will see the biggest rises of more than 4%, with NHS Forth Valley and Fife seeing above average increases, according to a new budget breakdown of health spending.
Nine out of the 14 regional boards will receive smaller increases of around 2.6%.
Special health boards, which have a national role in improving health, will either see their funding rise below inflation or have their funding cut.
Healthcare Improvement Scotland, which supports providers, and NHS Health Scotland, set up to tackle inequalities, will see their funding cut by more than 4%.
Other special boards will see rises of up to 1%.
Health Secretary Alex Neil said: "The Scottish Government is committed to protecting spending on health, and this budget allocation reflects an increase in real terms for every territorial health board across Scotland.
"This funding is part of an overall health budget totalling £12 billion. Investment in providing frontline care in our health service will ensure that we can continue to deliver the best possible care to patients across Scotland.
"Continued investment in buildings and equipment will also enable us to provide state-of-the-art facilities for patients and staff within our NHS.
"This demonstrates our excellent record of protecting investment in our NHS. By 2015-16, there will be an increase in resource spending of £2.1 billion since 2007, and between 2010/11 and 2015/16 the resource budget will have risen by 2.2% in real terms.
"However, it is right that despite protected budgets, the NHS is as efficient as possible with taxpayers' money.
"That is why health boards are making efficiency savings of 3%, with all savings being reinvested in front line care."
Over £370 million will be invested to improve NHS buildings and equipment.
Capital funding includes £111 million towards the New South Glasgow Hospitals project, which is due for completion in 2015; £8 million to Ayr and Crosshouse hospitals; £2.5 million on a new psychiatric unit in Fife; and £3.5 million to improve Inverness Raigmore Hospital.
Over £6 million is to be invested in replacement vehicles for the Scottish Ambulance Service, and £12 million in planned replacement of radiotherapy equipment across Scotland.
In addition, territorial health boards are to receive a 14.2% increase in their budgets for local priorities, including buildings maintenance and medical equipment replacement.