AP Photo/Matt Rourke
Donald Trump during a lunch stop in South Carolina in February.
The note undercuts earlier comments from Trump that suggested hope for a peaceful transition was diminishing.
"Today's call, like the others since the election, was positive and focused on continuing a smooth and effective transition," the White House said in the statement.
"The President and President-Elect committed to staying in touch over the next several weeks and agreed their respective teams would continue to work together to effectuate a smooth transition of power on January 20th."
Earlier on Wednesday, Trump appeared to turn on Obama over the president's comments that he would have defeated Trump in the election had he been constitutionally allowed to run for a third term.
"Doing my best to disregard the many inflammatory President O statements and roadblocks," Trump said in a tweet. "Thought it was going to be a smooth transition - NOT!"
A day earlier, Trump tweeted once more to dispute Obama's claim.
"President Obama said that he thinks he would have won against me," Trump said on Twitter. "He should say that but I say NO WAY!"
The comments were a turnaround from what appeared to be a conciliatory relationship between Trump and Obama. Since Trump began his transition to power in November, the two met at the White House, spoke on the phone multiple times, and before this week, were generally praiseful of the other.
Trump himself said his Wednesday phone conversation with Obama was "very nice" - further compounding the mixed signals.