The four-year-old is expected to make a full recovery after he was brought to the mainland in just under an hour by the crew of the Baltimore lifeboat.
A spokesperson for the RNLI said the swift operation was a remarkable achievement given the weather conditions.
It is understood the young boy, who had been ill for a number of days, had become very unwell overnight.
The island nurse assessed him and decided he required more advanced medical care on the mainland.
Weather conditions have forced the cancellation of several ferry sailings in recent days and the decision was made to task the lifeboat.
The crew was tasked by Valentia Coast Guard at 9.29am yesterday.
Coxswain Aidan Bushe along with five volunteer crewmen were launched in their powerful all-weather lifeboat within minutes of the alert.
They proceeded in poor weather conditions, against a swell of 3m and force six to seven northwest winds, to the North Harbour of Cape Clear Island.
When they arrived at the pier, the little boy, while conscious, had become listless and unresponsive.
He was immediately stretchered aboard the lifeboat, and in the company of his mother, was constantly monitored by lifeboat first aider, Jerry Smith, on the journey back to Baltimore.
Mr Bushe said while conditions were challenging, the patient was kept very comfortable on the return journey.
The lifeboat arrived at Baltimore pier at 10.30am, from where the boy was transferred to Skibbereen for medical attention.
He is expected to make a full recovery.