Hurricane Matthew's effect on fuel markets will be unknown for days, but gasoline prices could whipsaw in the coming weeks as the storm causes gyrations in supply and demand in the Southeast.

"Hurricane activity can have a mixed impact on supply and demand; while supply disruptions can be a bullish influence, the dent to demand caused by inclement weather can serve to offset this," ClipperData's director of commodity research, Matt Smith, told CNBC.

On Thursday, the average price of gasoline in Florida rose 2 cents from Wednesday to $2.178, and was up 4.3 cents from last week, according to GasBuddy.com. Prices were also up about a penny in North and South Carolina from Wednesday. Analysts said prices were spiking in part as regional distributors stocked up and consumers filled their tanks ahead of the storm, CNBC reported.

The storm is not expected to affect U.S. oil infrastructure or refineries, so supply will be largely unaffected. In fact, demand will likely fall in the coming days as drivers stay off the roads in the Southeast, said Tom Kloza, global head of energy analysis at Oil Price Information Service.

"This is a demand destroyer. That's the bottom line," Kloza told CNBC, noting that people don't drive in the rain the way they do in dry weather.

Meanwhile, Hurricane Matthew may delay petroleum cargoes to the U.S. East Coast by four days as ships stay in port while the storm passes, Bloomberg News reported.

“The New York Harbor market as well as markets along the southeast of the U.S. regularly receive foreign products cargoes,” Andy Lipow, president of Lipow Oil Associates, a Houston-based consulting company, said in a telephone interview. The disruption comes at a time when inventories are high and able to absorb a supply disruption, said John Mayes, an analyst at Dallas-based consulting company Turner Mason & Co.

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