The Prince of Wales said he was "delighted" to support the Trust, which works to improve the lives of the 10,000 people with cystic fibrosis across the UK through world-class research, care and advice.
Prince Charles' new patronage will be officially announced at a gala dinner on 8 May, which is being held in honour of the half-centenary.
Britain's future King is taking over the patronage from Princess Alexandra of Kent, who has worked with the charity for nearly 47 years, and will hold the position for five years before it is reviewed.
"Having for so long felt deeply about the suffering of cystic fibrosis patients, I am delighted to take on patronage of the Cystic Fibrosis Trust from Princess Alexandra in this, the Trust’s 50th year," said Charles in a personal message for the gala. "By funding ground-breaking research, improving the quality of care and providing invaluable advice and support, the Trust carries out extraordinary work on behalf of the 10,000 people with cystic fibrosis in the United Kingdom.
Prince Charles is taking over from Princess Alexandra
"The progress that has been made to improve the lives of people with this condition is a wonderful tribute to the determination of the sufferers and their families," he added. "As well as to the clinicians and health professionals, scientists and all those who support the Trust and its important work."
George Jenkins OBE, Chairman of the Cystic Fibrosis Trust, thanked Princess Alexandra for working with them for so long.
"We are extremely grateful to HRH Princess Alexandra for her support for the Trust over so many years," he said. "She has been a very important part of our organisation for most of its history, and on behalf of the whole of the cystic fibrosis community in the UK I wish to thank her for the wonderful support she has provided over this time."
Princess Alexandra of Kent was patron of the Trust for 47 years
"We are delighted that HRH The Prince of Wales has agreed to become the Patron of the Trust in our 50th year, especially as he has a deep understanding of the inspirational courage and determination of those affected by the condition," he added. "Today’s announcement comes at a time of extraordinary developments in cystic fibrosis research and as the Trust steps up the fight to beat cystic fibrosis for good."
Prince Charles was previously patron of an appeal established by the Trust in 2000 to help develop a new specialist cystic fibrosis unit at the Liverpool Heart and Chest Hospital.
The Prince opened The Amanda Unit, named after Amanda Roberts who died from cystic fibrosis at the age of 26 in 1998, in February 2002.