The issue of British relations with Libya and the row over the release of Megrahi from a Scottish prison last month was not on the agenda, Brown's spokesman told reporters on Thursday.
Obama and Brown have not spoken since late July, sparking British media speculation of a rift over treatment of Megrahi, who is dying from cancer and who was released by the Scottish authorities on compassionate grounds.
His release and joyous reception in Tripoli angered Washington and many relatives of victims of the attack. The bulk of the 270 people killed in the bombing of a Pan Am passenger plane over the Scottish town of Lockerbie in 1988 were American.
Britain said the matter was for the devolved Scottish government, but was accused of putting pressure on Edinburgh to help British companies win trade deals with Libya which has Africa's biggest proven oil reserves.
Brown will attend a meeting of leaders of the group of 20 nations in Pittsburgh later this month at which further measures will be discussed to help restore the global economy to health and banking regulation.
Asked about ties between Britain and the United States, the Prime Minister's spokesman said, The fact is, it is a very important and indeed special relationship.
(Reporting by Keith Weir; Editing by Louise Ireland)