A subatomic disruptor was a 29th century starship-mounted disruptor energy weapon which caused a target's molecular structure to break apart. It was capable of taking down the shields of an Intrepid-class starship in one hit.

In 2373, Captain Braxton, a Starfleet officer who had traveled back in time from the 29th century, attempted to destroy the starship USS Voyager with a subatomic disruptor, with which his vessel, the Federation timeship Aeon, was equipped. The Voyager crew was able to counter Braxton's attack by using their deflector to emit a high-energy polaron pulse, but Braxton managed to remodulate his disruptor, causing Voyager's deflector to lose power. Captain Janeway then ordered the deflector adjusted to match the frequency of the Aeon's disruptor, an act which had the effect of overloading Braxton's emitter. (VOY: "Future's End")

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