The awards, celebrating their eleventh year, recognise outstanding contributions made by education teams and individuals to help students around the country to succeed, both inside and outside the classroom.
Comedian and TV presenter Harry Hill was pictured with staff at the academy on the night.
The motto of Cathedral Academy in Wakefield is "greatness is within" - and judges said its pupils certainly have shown that to be the case.
Around half the Church of England secondary school's pupils are classed as disadvantaged, but their development over the past two years has put the school in the top 10 per cent for progress nationally.
"We teach our students to believe in themselves and that the skills they need to succeed are within their own potential," said the Academy's Principal, Rob Marsh.
"As a collective, we teach that everything is possible for one who believes," Rob said.
Bishop of Huddersfield, Rt Rev Jonathan Gibbs, who leads on education for the diocese, praised the Academy for its excellent result: "On behalf of the Diocesan Board of Education, I am delighted to offer warmest congratulations to Cathedral Academy in Wakefield on receiving the prestigious Best Secondary School award at the recent TES Awards Ceremony.
"This is a fabulous achievement.
"It is also wonderful news that Bradford Academy took the Community and Collaboration award at the same ceremony - another fantastic result.
"These two awards are a testimony to the dedication and commitment of the staff, pupils and whole community at these schools.
"They should be justly proudly of these outstanding achievements."
Such success in Wakefield has come despite a financial crisis two years ago, when a projected deficit of £500,000 meant that the school had to make many cutbacks.
Yet the school improved outcomes on almost every measure, and was able to maintain its much loved performing arts curriculum.
The judges praised staff for their "remarkable" achievements.
"This school has shown huge progress in a very short space of time," they said, and this was despite pupils coming "from one of the most deprived areas nationally".
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