He was born in Somersetshire, in England, to the Rev. Francis Charles and Emma Frances Johnson (James Brooke's younger sister).
Francis and Emma had several other children: Captain John Brooke Johnson-Brooke (older than Charles), Captain William Frederic Johnson, Henry Stuart Johnson Brooke, Mary Anna, Harriet Helena, and Emma (all younger than Charles).
Since James had no children, he named his nephews to succeed him as Rajah. In 1861, he named Captain John Brooke Johnson-Brooke, his sister's oldest son, as his successor. Two years later, he deposed and banished John from Sarawak (John was in England at the time) when John criticized him. In 1865, James named Charles as his successor.
Charles adopted his uncle's name and entered his service in 1852 as Resident at the Lundu station. On October 28, 1869, he married Margaret Alice Lili de Windt.
Charles continued the work his uncle had started, suppressing piracy, slavery, and head-hunting while encouraging trade and development and expanding his borders as the opportunity arose. By the time of his death, Britain had granted Sarawak protectorate status, it had a parliamentary government and a railroad, and oil had been discovered.
Charles was succeeded by his son, Charles Vyner Brooke.