The former secretary of state was asked about the exchange by the moderator yesterday, at an event in a Denver suburb.
Clinton said she did not second-guess people who make such tough decisions, but said the American tradition of caring for its citizens and soldiers was a "noble" one.
She also noted that countries like Israel have made similar swaps, citing that country's decision to exchange more than 1,000 Palestinian prisoners for one of its soldiers in 2011.
"This young man, whatever the circumstances, was an American citizen serving in our military," Clinton said. "The idea that you really care for your own citizens and particularly those in uniform, I think is a very noble one."
Several Republicans have hammered the Obama administration for the deal, saying it had capitulated to terrorists.
Additionally, some critics have suggested that Bergdahl deserted his post in Afghanistan before being captured by the Taliban in 2009.
Clinton said the most important thing will be to get as much information as possible from Bergdahl about his time in captivity, saying he could be a valuable intelligence asset and shed light on the Taliban's workings.
She noted the Guantanamo detainees were supposed to be kept in the Gulf emirate of Qatar for a year.
She added that she understood regrets about the deal but that the Obama administration feared Bergdahl wouldn't survive much longer. She described it as an example of the "hard choices" in government that is also the title of her forthcoming book.
"You don't want to see these five prisoners go back to combat. There's a lot that you don't want to have happen. On the other hand you also don't want an American citizen, if you can avoid it, especially a solider, to die in captivity," Clinton said. "I think we have a long way to go before we really know how this is going to play out."
Clinton appeared as part of a public speaking series called Unique Lives & Experiences.