Emergency services were called to the beauty spot at around 4.50pm on Sunday.
The Scottish Fire and Rescue Service sent two water rescue teams and two appliances to the scene where the pair were stuck in rapids.
Firefighters helped the first person to safety using a ladder and rescue lines.
The coastguard said the second person was rescued by coastguard teams and fire crew.
The fairy pools are a series of waterfalls and pools on the River Brittle at the foot of the Black Cuillins on Skye.
They have become popular as a place for wild swimming, drawing visitors from around the world.