Lynn McCallum is taking over that role from Cliff Sharp after he retires later this summer.
Dr McCallum, of Peebles, has worked for the regional health board for the past five years as a consultant physician based at the Borders General Hospital in Melrose, taking on the role of clinical director for unscheduled care services during that time.
She previously worked at Edinburgh Royal Infirmary.
Dr McCallum said: “Over the past five years, I have been privileged to work with many fantastic colleagues across NHS Borders and also to be welcomed as part of our thriving Borders community.
“I am truly delighted to take on the role of medical director and work with our board and health and social care colleagues to provide safe, effective, person-centred services.
“As we emerge from the Covid-19 pandemic, we have a real opportunity to build on some of the changes we have made and to redesign and rebuild healthcare services that meet the needs of our community.
“Involving colleagues and our communities with this work is critical, and I look forward to taking this forward in the coming months and years.”
Health board chief executive Ralph Roberts added: “I am delighted that Dr McCallum will be joining our executive team at NHS Borders.”
“She will bring her extensive clinical experience as well as her passion to the role, and I am looking forward to working with her to continue to modernise and improve our local health services in the Borders.”