Obama will address the interfaith service and by extension the country following the blasts that killed three people and wounded 176 in the worst attack on U.S. soil since September 11, 2001. No arrests have yet been made in the investigation.
Hundreds of people crowded outside the Cathedral of the Holy Cross in Boston's South End, about a mile (1.6 km) from the bombing site, before the service.
"President Obama knows how important the city of Boston is to the nation and the world," said 55-year-old John Snyder, who had joined the line before sunrise. "He is bringing his light to us for much-needed healing."
Dozens of uniformed police officers in bright yellow vests formed a security line around the church. City officials used buses to block access to nearby cross streets.
Local officials including Massachusetts Governor Deval Patrick, Police Commissioner Ed Davis and Congressman Ed Markey met Obama on the tarmac of Boston Logan International Airport as he stepped off Air Force Once and into the motorcade that would take him to the memorial service.
Obama was due to meet families of victims of the bombing and first responders while in Boston, a White House spokesman told reporters aboard Air Force One.
Boston Mayor Tom Menino, who has been making public appearances in a wheelchair since breaking a bone in his leg over the weekend; Patrick, and Cardinal Sean O'Malley will also speak at the service.
The service comes the day after the FBI arrested a Mississippi man in connection with letters believed to have contained the deadly poison ricin and sent to federal officials, including Obama. In a separate incident on Wednesday, an explosion at a Texas fertilizer plant killed as many as 15 people.
The FBI said there was no indication of a connection between the ricin letters and the Boston bomb attacks, but they reminded Americans of anthrax mail attacks in the wake of the September 11 suicide hijackings 12 years ago.
'All hands on deck'
US Homeland Security Secretary Janet Napolitano said on Thursday that authorities had stepped up security at airports, transportation hubs and other sites around the county and that the investigation was moving forward.
"This is an all-hands-on-deck effort by the entire federal government, led by the president," Napolitano said in Congressional testimony. "We are committed to bringing the perpetrators to justice."
Investigators believe the Boston bombs were fashioned out of pressure cookers and packed with shrapnel. Ten victims lost limbs, and emergency room doctors reported plucking nails and ball bearing from the wounded.
The suspect in the video had not been identified by name, two US government officials said.
Police had considered making an appeal to the public for more information at a news conference on Wednesday, a US government source said, but the FBI canceled it after a number of delays.
Boston Police and FBI officials said on Thursday that they had not determined whether they would publicly release more details of the investigation.
The bombs in Boston killed an 8-year-old boy, Martin Richard; a 29-year-old woman, Krystle Campbell; and a Boston University graduate student and Chinese citizen, Lu Lingzi.
Ahead of his visit, Obama declared a state of emergency in Massachusetts, a move that makes federal funding available to the state as it copes with the aftermath of the bombing.
The crowded scene along the race course in central Boston on Monday was recorded by surveillance cameras and media outlets, providing investigators with significant video footage of the area before and after the two blasts.
Based on the shards of metal, fabric, wires and a battery recovered at the scene, the focus turned to whoever may have placed homemade bombs in pressure cooker pots and taken them in heavy black nylon bags to the finish line of the world-famous race.
Tens of thousands of people turn out to watch and run in the marathon, which comes on a state holiday and is one of New England's best-attended sporting events.
"The president being here shows a sign of unity," said Mary Fitzgerald as she waited in line for the memorial service. "It makes me feel like he cares what happens to us."