Stanley sailed as scientific officer on Captain George Back's voyage in the Terror to the Arctic regions during 1836-37. This was Back's last expedition to find a sea route from Hudson's Bay to the Polar Sea, tracing the coast of the Polar Sea between Repulse Bay and Turnagain Point, the farthest point reached by Franklin on his first overland expedition. The Terror was caught in pack ice at the entrance of Fox Channel, west of Baffin Island, and stranded for 118 days on an ice floe, where she drifted 200 miles. The Terror was eventually brought out by passing chain cables under her keel and survived to sail again with the Erebus to the Antarctic under the command of Captain J.C. Ross.
Stanley's sketchbook from the voyage is in the National Maritime Museum, Greenwich.