Obama expressed his condolences to the prime minister.
"The president reiterated his condemnation of the barbaric attack," the White House statement said. "He offered his support for the ongoing investigation, and for the Bulgarian people in this challenging time.
"The leaders discussed the strong partnership and excellent counterterrorism cooperation between the United States and Bulgaria, and the president expressed his appreciation for Bulgaria's important contributions as a NATO member to international peace and security."
U.S. officials say the suicide bomber who killed six people, including five Israeli tourists, on a bus Wednesday appeared to have been a member of Hezbollah.
The New York Times said a source who wished not to be identified while the investigation was under way said it appeared the bomber was in Bulgaria looking for opportunities to attack Israeli targets.
Bulgaria is a popular vacation spot for Israelis and Burgas is on the Black Sea, the BBC said.
The Times source said it appeared the militant group received guidance from Iran, the group's primary sponsor. The newspaper said two other U.S. officials confirmed Hezbollah was behind the bombing.
An official said it appeared the bombing was in retaliation for the assassinations of Iranian nuclear scientists, which Iran alleges were committed by Israeli agents.
An Iranian Foreign Ministry spokesman Thursday said Tehran strongly condemned "all terrorist acts." Hezbollah has not publicly commented, the BBC reported.
Interior Minister Tsvetan Tsvetanov said the man was in Bulgaria for at least four days prior to the terror attack and may have had an accomplice, Sofia News Agency reported.
Besides the seven people killed, including the bomber and the Bulgarian bus driver, 30 were injured when the bus carrying Israeli tourists exploded in an airport parking lot.
Security footage of the suspected bomber released by Bulgarian officials shows a white male with long hair walking in the airport terminal with a backpack, the BBC said.
The Times said the bomber had a fake Michigan driver's license, but there are no indications he had any connection to the United States.
"This looks like he was hanging out for a local target, and when this popped up he jumped on it," a U.S. official said.
Israeli Prime Minister Binyamin Netanyahu said Thursday the attack was carried out by "Hezbollah, the long arm of Iran."