"We worked in full transparency with the regulator," Vounatsos said on "Squawk Box," emphasizing that the FDA has all of the company's data on the drug.
"The evidence came over time. We collected a tremendous and complex set of data, including biomarkers and imaging," he said. "This was a thorough engagement, and as CEO I'm reasonably confident this will lead to market approval one day."
Shares of Biogen soared more than 26% on Tuesday after the drugmaker shocked investors by announcing it was seeking regulatory approval for its once failed Alzheimer's drug, aducanumab. The shares were up less than 1% midday Wednesday.
In March, the Cambridge, Massachusetts-based company said it halted two late-stage trials for its drug after an analysis from an independent audit revealed the drug was unlikely to work.
Biogen lost billions of dollars in market value at the time. The scientific community viewed the announcement as a setback after spending billions to research and develop possible treatments — with almost nothing to show for it. Patients and families living with the disease who had pinned their hopes on aducanumab were heartbroken.
Alzheimer's disease can cause people's memory and mind to deteriorate to the point where they cannot function on their own and eventually die. It's the sixth leading cause of death in the U.S., and the Alzheimer's Association estimates 5.8 million Americans are living with the disease.
There are currently no drugs approved that can reverse the mental decline from Alzheimer's. The FDA has approved Alzheimer's drugs aimed at helping symptoms, not actually reversing or slowing the disease itself.
Biogen's experimental drug targets a compound in the brain known as beta-amyloid, which was believed by many scientists and drugmakers to play a role in the devastating disease by eroding synapses between nerve cells.
On Tuesday, Biogen said a new analysis of a larger dataset showed that aducanumab "reduced clinical decline in patients with early Alzheimer's disease" and patients who received the drug "experienced significant benefits on measures of cognition and function such as memory, orientation, and language."
The findings were met with skepticism from investors who said the results may have just been by chance. But the stock surged anyway on hope for approval.
Vounatsos insisted that Biogen's dosing of the drug previously just wasn't high enough. "The road to breakthrough innovation if full of twists and turns," he added. "We started to have some hope."