Channel 4 chief executive David Abraham received a £100,000 bonus last year, partly thanks to the success of the Paralympics.
The bonus was paid on top of Abraham's £515,000 salary, and with benefits of £129,000, he received a total of £744,000, compared to £701,000 in 2011.
Abraham's salary is higher than that of BBC director general Lord Hall, who is paid £450,000-a-year.
The figures, revealed in Channel 4's annual report, shows that the broadcaster's chief creative officer Jay Hunt's total pay went up from £487,000 in 2011 to £542,000, including bonuses of £116,000.
A one-off reward, amounting to 2.5 per cent of the total bonus, was paid to all staff on account of the broadcaster's Bafta-winning coverage of the Paralympics, which was watched by almost 40 million people.
Total aggregate gross salaries went up from £37 million to £55 million at the main channel, Channel 4, while at the Channel 4 group it increased from £52 million to £55 million.
The commercially-funded, not-for-profit broadcaster said that total content spend was £608 million - up 3 per cent - for the year.
Spending on originated content across all Channel 4 services reached £434 million, up 4% from the last year.
Channel 4 reported a loss of £29 million for 2012 while the Channel 4 group reported a £27 million loss, as part of a planned programme of investment.
The broadcaster's main channel's total share of viewing was 6.6 per cent last year.
With its digital TV channels, which includes E4, it had an 11.5 per cent share of viewing, down 1 per cent.
The broadcaster has enjoyed success with US drama Homeland, university sitcom Fresh Meat and six-part drama My Mad Fat Diary and recently won gongs at the TV Baftas for the likes of Made In Chelsea, its Paralympics coverage, and funnyman chat show host Alan Carr.
Channel 4 chairman Lord Burns said: "The board is very pleased with the creative performance in 2012. Of course the Paralympics stand out, not only as a highlight of the year but in Channel 4's entire history. They exemplify much of what Channel 4 was originally established to do and what it continues to stand for today.
"We took a bold risk to transform the Paralympics as a sporting event and to shift attitudes towards disability."
He said of the financial rewards: "The committee seeks to balance (the need to) reward commercial success while being sensitive to the position that Channel 4 occupies as a publicly-owned organisation."
He said success had taken place "against a very tough economic climate" and that changes in executive pay were "relatively small".
Abraham, who chose to reduce his maximum bonus potential from 50% to 30% in 2011, said: "If you compare Channel 4's performance in 2012 versus its commercial competitors we fared pretty well."
He said that Channel 4 set its pay "between the state funded sector and the commercial sector" but that it was set at "nearer the state-funded sector".
"We are a hybrid. We're not receiving a cheque from the Government every year," he added.
Asked about receiving more than Lord Hall at the BBC, he said: "It's difficult to compare apples and pears because of the pension schemes at the BBC."
He said that following the Paralympics "a number of broadcasters from around the world have asked us how they can do the same for their country".