The announcement was made after national judge Cate Prestidge viewed footage of schools that placed at every event throughout the country.
She focused on concept, soundtrack and drama when determining the awards.
"I don't even know what went through my mind when we found out we had placed nationally - it was such a shot out of the blue for us but we are so excited," Xianar Pike, 17, said.
Rotorua Girls' High School's performance centred around Te Arawa history and how it has shaped society. The students depicted figures including Hinemoa and Tutanekai, Hatupatu and Patupaiarehe, as well as historic moments like the Tarawera eruption.
"We wanted a theme that had a strong meaning to the school and our Maori culture and we feel like we did that justice," Sally said.
Teacher and Stage Challenge director Janaye Biddle-Kite said she was "beyond proud" of the team.
"I admit we were bummed about getting third this year, especially because we won last year so to place nationally - a first for Rotorua Girls' High School - has really lifted the bar for us.
"Stage Challenge is such a long haul and by the end of it, the whole team is exhausted so once it was over, we just started looking towards next year's production. To be recognised nationally was a huge shock but a major achievement for us."
National Awards:
First: Wanganui High School
Second: Tauranga Girls' High School
Third: Rotorua Girls' High School, Hawera High School
Excellence for Concept: Whangarei Girls' High School
Excellence for Drama: Bream Bay College
Excellence for Soundtrack: Sacred Heart Girls' College (Hamilton)
Backstage Crew Winners: Mount Maunganui College, Wairarapa College
Excellence for Student Leadership: Pieta McAleer-Harding (Christchurch Girls' & Boys' High School combined)