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John Boehner just made Janet Yellen's life harder

John Boehner's decision to relinquish his House leadership post inadvertently complicates things for the Federal Reserve.

The impact over the Boehner move involves a subplot regarding a potential government shutdown.

In short, his decision decreases the chance for an October shutdown but increases the odds of a December close, making it more difficult for the Fed to enact a long-awaited interest-rate hike.

"This improves the chances that there will be no shutdown next week," said Greg Valliere, chief political strategist at Potomac Research Group in Washington, D.C. "However, I think the chances of a really serious crisis in mid-December have gone up quite a bit."

Democrats and Republicans once again are squaring off over the future of national fiscal policy, with the GOP clamoring for spending cuts and the end of subsidies for Planned Parenthood, both of which have met stiff resistance on the other side of the aisle.

Janet Yellen and John Boehner
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Janet Yellen and John Boehner

Republican Boehner has been at the center of multiple other similar struggles, with this one particularly testy heading into a presidential election year. Valliere thinks Boehner actually could act as a peacemaker on his way out the door. However, that atmosphere likely will change under his successor, expected to be Kevin McCarthy of California.

Read MoreBoehner: Leadership turmoil could do harm

"Boehner will go to (minority leader) Nancy Pelosi if he has to, to get votes from Democrats. What does he care? He's leaving," Valliere said. "It will be easier for him to get votes for a continuing resolution that lasts until Dec. 11."

While the congressional wrangling unfolds, Fed Chair Janet Yellen and her fellow central bankers will be plotting a way to escape seven years of zero interest rates.

In a much discussed speech Thursday, Yellen again indicated the Federal Open Market Committee was ready to hike its key funds rate before the end of the year. However, the FOMC only has two meetings left: one in October, when a hike seems highly unlikely for a variety of reasons; and the other in December, which would come just a week after the government shuts down.

Read MoreSo why all the fuss over what Yellen said?

"The risk of disruption to the economy and/or financial markets from another debt ceiling standoff is another reason to suspect that the Fed definitely won't hike interest rates in October and possibly may even stand pat in December, too," Paul Ashworth, chief U.S. economist at Capital Economics, said Friday in a note to clients.

For investors, that means likely more volatility as market participants continue to be left guessing by the course of Fed policy.

"If the markets hate uncertainty, there's real uncertainty looming in December because of the Fed angle," Valliere said. "The market will really start to pay attention to this story after Thanksgiving."