Speaking at the POLIS Value of Journalism conference, Boaden acknowledged that impartiality "is not a simple thing".
"It is often in the tone and language and people often don't realise they are taking sides," she said.
But she defended the broadcaster's stance, claiming that impartiality was "the core" of the BBC's journalism.
She also defended the BBC editorial policy unit, set up in the wake of the Hutton inquiry, which has led to the broadcaster being criticised as "risk averse".
Boaden said that the unit did not weaken the BBC's journalism, but strengthened it by protecting the broadcaster from accusations of impartiality.
She cited the recent Panorama investigation into abuse at a care home for people with learning difficulties, which she called "a profoundly difficult journalistic endeavour".
The programme, which was based on five weeks' worth of secret filming by an undercover reporter at the home, led to four arrests, 13 members of staff being suspended and government inspections.
Boaden praised undercover reporter Joe Casey, and said that the programme was "a very very tough call on any journalist".
Asked by chair Krishnan Guru-Murthy whether the BBC would remain impartial, despite its competitors taking a different approach, she said that "it absolutely will".
"The BBC has survived for as long as it has and the core of that it impartiality."
"Our values demand impartiality. We don't always get it right but we work at it very hard on a daily, even hourly basis.
Her address at the conference stressed the importance of journalistic confidence, which she said would not be affected by the looming job cuts at the broadcaster.
The merger of the the BBC's domestic and global news teams would be "painful", she said, admitting that job cuts "always leave people feeling down", but she claimed that the cutbacks would not affect the confidence of BBC's journalists, which comes "from getting things right".
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