The £200,000 fund will be available to NHS boards across Scotland, Health Secretary Alex Neil said on the eve of a conference exploring the issue.
"Across our NHS, much has been done to tackle bullying and harassment in the workplace. However, feedback suggests that bullying and harassment may still be an issue across our workplace," he said.
"I am very clear that we will not tolerate bullying of any kind in our NHS. It is not good for our hardworking NHS staff and it is not good for patients."
The funding is said to be aimed at improving dignity in the workplace.
A free, confidential phone line for NHS staff who wish to raise any concerns about practices in the NHS is being piloted.
The alert line allows staff to discuss and report concerns they may have about patient safety and malpractice in the knowledge that their identity is protected, according to the Scottish Government.