Lee will oversee all factual commissioning for Channel 4 in a new department encompassing both the documentary and specialist factual teams.
His appointment follows the decision by Mykura, the former head of documentaries and More4, to move on after a decade at Channel 4.
Channel 4 said that it will now advertise for a deputy head of factual, a new role that will support Lee as head of factual.
Channel 4 chief creative officer Jay Hunt said: 'We have been working hard to make Channel 4 more accessible to suppliers and this new structure will streamline the factual commissioning team and speed up the time it takes to get back to producers.
"Previously there was considerable overlap between departments with suppliers often pitching the same ideas to a number of teams. The new structure creates a one-stop-shop for factual and ensures there is more co-ordination, as well as cross-fertilisation, between the different genre areas within it."
Lee joined Channel 4 in September 2002 as a specialist factual commissioning editor and was responsible for shows such as living history series That'll Teach 'Em and Deep Water, the tragic story of round-the-world yachtsman, Donald Crowhurst.
He left Channel 4 at the end of 2007 to become head of factual at Channel 5, but returned to the broadcaster as head of specialist factual in May 2008. His most recent commissions have included Inside Nature's Giants, Four Rooms and Food Hospital.
Hunt added: "Ralph is a formidable creative leader and a superlative manager. His knowledge and enthusiasm across a wide range of specialisms as well as his substantial track record for bringing fresh approaches to factual television make him the ideal person to take Channel 4 factual on to the next level."