The stock market may not get the post-midterm surge over the next 12 months that usually happens, Wharton School finance professor Jeremy Siegel warned on Tuesday.

"There's a lot more uncertainties that will make next year not ... a stellar year we usually get in third-year presidential cycles," Siegel, a longtime stock bull, said in a "Squawk on the Street" interview.

Siegel blames worries about the Federal Reserve's path higher for interest rates and the possibility of Democrats taking control of the House in Tuesday's voting.

Democrats are expected to win the House, while Republicans are expected to keep their slim majority in the Senate.

Stocks have already reaped the benefits of President Donald Trump's business-friendly deregulation and tax cuts, said Siegel, though he did admit that the market has historically done well under a divided government.

On average, the has been up 16.7 percent in the 12 months after midterm elections, going back to World War II, according to CFRA. (Of course, past performance is not indicative of future results.)

Stocks were higher Tuesday as investors awaited the results of the much-anticipated election.

The Dow Jones Industrial Average and the S&P 500 on Monday logged their fourth positive sessions out of the past five, with the Dow closing at its highest level in nearly three weeks.

Last month, Siegel urged investors to be somewhat cautious, saying numerous headwinds, including the midterms, will keep stock prices muted for 2019.

However, at the time, Siegel said he still favors stocks long term, adding the market will be the best-performing asset for investors looking out three to four years from now.