Alongside Heughan and his co-star Catriona Balfe, who played his time-travelling love interest, two other executive producers will be given the special Bafta award.
Ronald D. Moore will receive it for his role in adapting the story from Diana Gabaldon’s original novels into the TV format.
He said: “It has been a tremendous pleasure to work with our Scottish crew, to utilise the Scottish locations and to learn more about Scottish culture and history.
“It’s been a huge joy for all of us on the production.”
American showrunner Matthew B. Roberts added: “When we first landed in Scotland, we were outsiders – Sassenachs – strangers in a strange land telling a very Scottish story.
“What we found was a country that opened its doors and a crew that opened their hearts.
“They welcomed us, guided us when we needed it, and made us feel like we belonged.
“Thirteen years on and I don’t feel like a visitor when I step off the plane; I feel like I’m home.”