The men, who are in their mid 20s, were caught in squally conditions after they left Raasay at about 20:00 on Sunday to paddle across about a mile of sea.
The mother of one of the men raised the alarm before later finding them on the shore of The Braes peninsula on Skye.
The Coastguard said the men were "very  cold" and needed medical attention.
The Portree RNLI lifeboat and Coastguard Rescue Team had been looking for the two men.
After the kayakers were found, the lifeboat crew took them to Portree Hospital where they were treated for hypothermia and cuts and scrapes.
The Coastguard team escorted the mother and another woman safely back home.
Coastguard watch manager Martin Collins said: "These kayakers have been very lucky.
"We have had wintery squalls across the area this evening with winds gusting to over 40mph at times and if they hadn't made someone aware of their plans they could have been exposed to the elements for a lot longer.
"If you are heading out to sea in a kayak the Coastguard recommends that you check the weather forecast and tidal conditions before you head out, wear a buoyancy aid and carry distress flares are in date and stowed where you can reach them."
He added: "For remote locations carrying a personal locator beacon is highly recommended."
Two kayakers got into difficulty after their craft capsized in bad weather while making an evening crossing between the isles of Raasay and Skye.