Yassin Mutegombwa, 22, of Upper Norwood, London, is charged with three counts of receiving terrorism training.
Police allege he was trained in the use of weapons in woodland near a caravan and campsite in Hampshire, and at another location in Berkshire.
Hassan Mutegombwa, 20, also of Upper Norwood, is charged with one count of procuring funds for terrorism.
The overnight raids staged on 1 September, which saw arrests at a Chinese restaurant in the Borough area of south London, were targeted at alleged terrorist recruiters, Scotland Yard has said.
Anti-terrorism officers also swooped on the Jameah Islamiyah Secondary School in Mark Cross, near Crowborough, East Sussex, which they continue to search.
Sussex Police said investigations at the school could take weeks but that no arrests had been made there.
The school was set up in 2003 as an Islamic teaching facility for boys aged between 11 and 16, according to Ofsted inspectors.
BBC home affairs correspondent Margaret Gilmore says the charging of one of the men has made legal history.
"One of the men has been accused of funding terrorism under a law which has been used before but the second man is accused for the first time under a specific part of the Terrorism Act 2006 with receiving training for the purposes of terrorism."
The two men were charged at Paddington Green high security police station in London and will appear in court on Tuesday.
The Metropolitan Police have been granted a warrant for the further detention until Wednesday of another man arrested in the raids.
A total of 14 arrests were made in the operation, 12 of them at the restaurant, and two people have since been released.
Among those being held is Abu Abdullah who is a former associate of the radical Islamic cleric Abu Hamza.
Police said the arrests were not connected to the alleged plot to blow up transatlantic airliners or the Tube and bus attacks in London on 7 July last year.
These are getting weekly events, glad we ae catching so many before they are able to partake in whatever sick thing they were planning