The organization announced the endorsement of its political action committee on Wednesday.
"Pro-choice Americans have been fortunate to have two strong pro-choice candidates in Senator Obama and Senator Clinton, both of whom have inspired millions of new voters to participate in this historic presidential race," NARAL president Nancy Keenan said in a statement. "Today, we are proud to put our organization's grass-roots and political support behind the pro-choice candidate whom we believe will secure the Democratic nomination and advance to the general election. That candidate is Senator Obama."
Clinton communications director Howard Wolfson said he was surprised by the group's decision to back Obama.
"Senator Clinton's leadership and advocacy on choice issues is second to none," Wolfson said.
Officials said NARAL's political committee board was about evenly divided among Clinton and Obama supporters and that the decision to endorse was hard fought. Ultimately, the board voted unanimously to support the Illinois senator.
NARAL officials said the decision wasn't intended to be a snub of Clinton, who is running to be the first female president.
They said the board decided to back Obama over Clinton because he is overwhelmingly favored to win the nomination and to heal what the organization viewed as a growing rift between black voters and white female activists that the protracted Clinton-Obama contest may have caused.
The organization endorsed Massachusetts Sen. John Kerry in 2004 when he was well on the way to securing the party's presidential nomination.