Dr Aaron Columbus, who is at present the deputy principal at Wellington College, is set to begin his new role at the start of term 4.
He said he was excited to be joining John McGlashan which he considered a school with a "deep history".
"It’s an opportunity to lead it into its next chapter and build on the work done by those who have come before me."
He had admired the school for a while and was keen to work with the school’s community.
Dr Columbus grew up in the Teviot Valley and his wife grew up on a farm near Roxburgh Dam and both were looking forward to returning to the region.
Board of trustees presiding member Geoff Burns said the school went through a rigorous recruitment process.
He said the appointment committee unanimously decided Dr Columbus was the right person.
"He is a seasoned academic and educator and has a clear vision around boys’ education that aligns well with John McGlashan’s ideology around assisting boys to become the very best they can be."
Before his appointment at Wellington College, Dr Columbus was studying and working in England.
