The Court of Appeals in Albany agreed without comment to review appeals against the upstate towns of Dryden, near Ithaca, and Middlefield, near Cooperstown.
The case is expected to be heard in the spring.
An intermediate-level appellate court in Albany in May affirmed lower-court rulings upholding the bans.
The mid-level court ruled state mining and drilling law does not supersede municipal rights to zone land and keep the industry out.
Some property owners -- including a farmer in the appeal to the state's high court -- oppose the municipal bans because they want to lease their mineral rights to drillers.
More than four dozen state municipalities ban such drilling and more than 100 others have moratoriums on drilling activities.
New York has a 5-year-old moratorium on fracking as state health officials study its effects. Democratic Gov. Andrew Cuomo's administration is weighing whether to allow large-scale fracking in parts of the state.
Fracking, a term the energy industry considers pejorative, is a technique to extract oil and gas from rock by injecting high-pressure mixtures of water, sand or gravel, and chemicals.
The decision by the state's high court to take the case is "a good sign," said Tom West, a lawyer representing gas company Norse Energy, the plaintiff in the suit against Dryden.
"It doesn't matter how many judges ruled against us. It's a matter of law and it's a fresh look at the issue," he told the (Rochester, N.Y.) Democrat and Chronicle.
Much of central and western New York sits atop the gas-rich Marcellus Shale formation, which holds 141 trillion cubic feet of gas reserves -- enough to meet consumption across the entire country for almost six years, the U.S. Energy Information Administration says.