An early settler at Moyale was a Greek by the name of Zaphiro, who had a station which he had named "Fort Harrington". When C.W. Gwynn visited in 1908, Zaphiro's station consisted of a garden that covered several acres and his house, located on a spur projecting from the Boran highlands, and providing access through the line of cliffs that run along the border. "This route may well become some day a considerable trade artery," Gwynn predicted. "Fort Harrington is therefore well placed as a healthy administrative post and as a possible commercial centre."
During World War II, both parts of the town was captured by Italians from Ethiopia in 1940, and retaken by the British on 15 July 1941. Tensions rose in the Kenyan side of Moyale in early 1999, after an Imam was shot dead during an Ethiopian raid across the Ethiopian-Kenyan border in pursuit of rebels of the Oromo Liberation Front (OLF). The Kenyan residents of the town, held demonstrations condemning the action, which they attributed to Ethiopian security men who believed he was a sympathizer of the OLF.
In November 2009, Ethiopian Prime Minister Meles Zenawi announced plans to extend the Ethiopian railroad to Moyale. This would facilitate Kenyan plans, which at the time were at an advanced stage, to develop the port of Lamu and connect it to the Kenyan side of Moyale with a tarmac road.
Moyale saw four days of ethnic clashes in July 2012 over a long-standing land dispute between Borana and Garri communities,exacerbated by drought conditions. The fighting left at least eighteen dead, and more than twenty thousand people fled across the border into Kenya
