Longtime stock bull Jeremy Siegel is urging investors to be cautious, saying numerous headwinds will keep stock prices muted for 2019.

"There are challenges that we face now," including rising interest rates, the midterm elections and U.S.-China trade tensions, the Wharton School finance professor said in a CNBC "Squawk Box" interview on Monday. "I'm looking flattish" for the coming year, he added.

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

"The sell-off in emerging markets has presented unbelievable value" in the near term, Siegel said.

U.S. stock were higher in early trading Monday. Last week, the Dow Jones Industrial Average and managed to break three-week losing streaks, but the Nasdaq fell for a third straight week.

The S&P and Nasdaq are on pace to post their largest monthly losses since January 2016 after the Oct. 10-11 plunge.

Concerns that Federal Reserve Chairman Jerome Powell might raise rates more than forecast has fueled stock declines and criticisms from President Donald Trump.

The central bank has hiked rates three times this year, and one more is expected in December.

Siegel told CNBC he worries how the Fed can engineer "a soft landing" as it continues to gradually increase rates in an effort to preserve a steady economy.

Siegel predicted last month the stock market could be headed for another bubble, like the one investors experienced in January. In early February, stocks plummeted and eventually bottomed later that month.