The images of Kerberos and Styx, the smallest of Pluto's five moons, were captured from more than 55 million miles away using the spacecraft's long range camera.
The photos were then processed to remove background stars and the glare of Pluto and the larger moon Charon, according to NASA.
Capturing the faint moons is an important step for NASA as it moves closer to the dwarf planet.
The techniques used to refine the images will be an asset to the New Horizons team. As the probe approaches Pluto, they will be on the lookout for new moons or rings that could be in the spacecraft's path.