The conversation was the first between the two leaders about the release of Libyan spy Abdelbaset Ali Mohmed al-Megrahi from a Scottish prison on compassionate grounds because al-Megrahi has terminal cancer, The Scotsman said.
A spokesman for the prime minister's office said Brown made it clear the decision was made by the Scottish government.
After the call, White House spokesman Robert Gibbs said Obama "expressed his disappointment over the Scottish executive's decision to release convicted Pan Am 103 bomber al-Megrahi back to Libya."
Al-Megrahi was convicted of killing 270 people in the air and on the ground when Pan Am Flight 103 when it exploded over Lockerbie, Scotland, in 1988.
The phone call between Obama and Brown was to discuss preparations for the Group of 20 economic summit in Pittsburgh later this month and to discuss the global economic situation, The Scotsman said.
"The two leaders concluded that the special relationship was as strong as ever and that there continued to be good co-operation across the full global agenda," Brown's spokesman said.