lthough less a seaman than a soldier, having served the Queen in Ireland as that capacity (and doing so again immediately following Frobisher's expeditions), Edward Fenton was made Captain of the ship Judith and Lieutenant General of the entire fleet during Frobisher's 1578 voyage, thus being Frobisher's second-in-command. In that role he recruited the miners for the expedition, was in charge of the troops assigned to the mission, and was to have commanded the new colony intended to winter on Kodlunarn Island.

Originally with sufficient supplies for eighteen months, about 100 men including miners, shipwrights, carpenters and soldiers, as well as the ships Judith, Gabriel and Michael, were to remain through the winter of 1578-1579 to protect the mines and perhaps locate more ore. Fenton was to keep a journal of observations on the nature of the land, the weather and the ice in "Frobisher's Strait". The loss of construction materials and provisions prevented the realization of this plan.

Although Fenton offered to stay with a smaller contingent, the mission's masons and carpenters reported that there was not enough time to build proper accommodations even for a smaller colony, with only a few weeks left of the summer season. Fenton had to content himself with ordering the construction of one small house on Kodlunarn Island, to test the sturdiness of English construction methods in an Arctic winter and to placate the Inuit through gifts left inside; both reflected the expectation of a further colonization attempt the following year. The structure was referred to as "Fenton's Watchtower". Fenton returned to England with the rest of the fleet.

Frobisher may have perceived Fenton as a potential rival. The two men certainly found themselves holding opposing opinions or judgements on occasion; one quarrel led to Frobisher attacking him with a knife. Not surprisingly, Fenton ended up in the camp hostile to Frobisher once the venture had deteriorated to assigning blame for its failure.

The Privy Council appears to have trusted Fenton more than it did Frobisher. Fenton's calmer, more systematic and scientific manner was illustrated in his translating and publishing Boasistuau's ancient work Certaine Secreate Wonders of Nature in 1569, in his careful search for additives needed by Burchard Kranich in 1577, and in his work in early 1578 on identifying and cataloguing ores discovered at a Cornish mine.

The Earl of Leicester proposed a new expedition to reach Asia, following the southwest route through the Straits of Magellan and across the Pacific. Frobisher had originally been nominated to command the expedition, but the Privy Council had lost confidence in him. Edward Fenton was chosen instead. The resulting voyage of 1582-83 was a costly failure. During the Armada campaign Fenton captained a ship whose construction had originally been commissioned by one of Lok's brothers, before its sale to the navy.