The 22-year-old has spent pre-season with the Cumbrians, but an agreement with Gateshead was not initially reached.
However, the two clubs have now agreed a fee and Gillies has signed a two-year deal.
"The clubs have worked closely together over the last few weeks to make sure we could resolve the issues amicably and we're pleased to say that is now the case," Carlisle managing director John Nixon said.
Sunderland-born Gillies, who joined Gateshead from Whitley Bay, scored 15 goals for Gateshead last season.
- Sports & Recreation