The BBC sitcom beat off stiff competition from The Big Bang Theory, Benidorm and Orange Is The New Black to claim the gong.
The programme’s creator and star, Brendan O’Carroll, said he was thrilled to have been recognised by the public.
Taking to the stage, he gushed: ”Thank you so much to all of you who voted, it's really important that you vote, this is the most important award we get.
"It's very, very exciting and very humbling. Thanks to the BBC and everyone involved."
However, despite the cast’s joy, those at home detected jeering among the audience as Sir Ken Dodd named Mrs Brown’s Boys as the winner.
One social media user observed: “Crowd actually booing Mrs Browns Boys there #NationalTelevisionAwards.”
“Sounded like Mrs Browns Boys got booed by quite a few in audience. Cant say ive ever found the show funny either #NTAS,”(sic) another commented.
While someone else said: “@hoskas Mrs Browns Boys was booed.”
Mrs Brown's Boys won the award for most popular comedy show at the National Television Awards
The sitcom's creator Brendan O'Carroll thanked viewers for voting
Viewers said Mrs Brown's Boys was booed by the audience
It's very, very exciting
Nonetheless, many watching at home were thrilled the Dublin-based drama had been given some recognition.
“Yes!!! @MrsBrownsBoys so deserved that! So funny&such lovely ppl,”(sic) one fan enthused.
A second agreed, adding: “Aww glad @MrsBrownsBoys got an award tonight. They are so dedicated and lovely 🙂 great bunch. Great vibes.”
The 51-year-old was met with a chorus of boos as he entered the stage with his GMB co-star Susanna Reid.
The audience booed Good Morning Britain presenter Piers Morgan
National Television Awards 2017: Arrivals
Wed, January 25, 2017
Celebrities arrive for the NTA's 2017
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One viewer said: “Piers Morgan getting boo'd by 20,000 people at the NTA's is all the satisfaction I need for a Wednesday night #NTAs.”
“Boo the f*** out of piers Morgan,” another demanded.
A third added: “Good to hear the boo's for Piers. What a pr***. #NTAS #NTAs2017.”
Catch the full programme on the ITV Hub.