Cook Political Report on Wednesday said Clinton had 62,403,469 votes compared to Trump's 61,242,652 votes.
Clinton's victory in the popular vote has generated criticism against the United States' Electoral College system. Following the 2016 election, Clinton's loss is the fifth time in U.S. history a candidate who won the popular vote did not assume the presidency. The last time was in 2000, when former Vice President Al Gore defeated then-Texas Gov. George W. Bush in the popular vote, but lost the recount in Florida -- giving Bush the needed electoral votes to win the executive branch.
Trump on Tuesday defended the Electoral College, despite calling the system a "disaster for a democracy" in 2012.
"If the election were based on total popular vote I would have campaigned in N.Y., Florida and California and won even bigger and more easily," Trump wrote on Twitter. "The Electoral College is actually genius in that it brings all states, including the smaller ones, into play. Campaigning is much different!"
Votes were still being counted in several states.