He feared the "political cost" would be too much, he said.
“I told [Obama] up front ... If you’re doing this, you can’t do this, this and this," Emanuel told the Chicago Sun-Times.
"And you’ve got to weigh that, and can you still achieve something on healthcare vs. also still trying to get other things done?" he said.
Emanuel added that Thursday's decision — in which the Republican-appointed chief justice sided with the court's liberals to uphold most of the law — was "rich with irony."
"I would like to take one minute to step back and acknowledge the type of courage it took," he said.
"For 60 to 70 years, president after president of both parties tried to achieve what President Obama has achieved."
He said he had already emailed Obama to congratulate him on the victory.