BioMarin's Jean-Jacques Bienaime said the company's hemophilia treatment could fundamentally change the quality of life for patients struggling with the disease.

Hemophilia A is a genetic disorder caused by a missing or defective clotting protein known as factor VIII, which can lead to excessive bleeding after an injury.

BioMarin has been having marked success in the space. Its treatment recently entered Phase 3 late-stage studies, which would support U.S. and European marketing applications.

"The cure word is a big world, but I would say the data we just reported recently at the American Society of Hematology meeting in December is extremely encouraging," Bienaime said. "We took patients that had less than 1 percent of factor VIII expression ... to, for the vast majority of them in the kind of normal range, 50 to 150 percent expression."

Bienaime spoke with CNBC at the annual J.P. Morgan Healthcare Conference in San Francisco.

Despite the progress in its hemophilia treatment, the company's shares have only climbed 2 percent in the past 12 months.

To be sure, while only a small number of patients have received the treatment to date, Bienaime said that such a dramatic increase in factor VIII expression allows patients to participate in physical activities otherwise deemed too dangerous for those living with the disease.

"Hemophiliac patients today, although they can be treated with recombinant factor VIII injections, they are very careful about their physical activity," added the CEO. "Here we have patients that now have normal physical activity."

While the BioMarin chief did not address questions about the potential price of the gene therapy — called valoctocogene roxaparvovec — Bienaime did address the concerns broadly.

"I think most of the rhetorical issues have been around egregious price increases. That not our business model," he told CNBC. "Generally, we have increased our price in the U.S. around inflation in the past five years. We don't take all molecules and dramatically increase the price of the item. That is not what BioMarin does."