At the outbreak of World War II, Wingate was the commander of an anti-aircraft unit in Britain. He repeatedly made proposals to the army and government for the creation of a Jewish army in Palestine which would rule over the area and its Arab population in the name of the British. Eventually his friend Wavell, by this time commander-in-chief of Middle East Command which was based in Cairo, invited him to Sudan to begin operations against Italian occupation forces in Ethiopia. Under William Platt, the British commander in Sudan, he created the Gideon Force, an SOE force composed of British, Sudanese and Ethiopian soldiers. At Khartoum, Wingate and Tony Simonds joined Mission 101 controlled by London and Cairo.

Gideon force was named after the biblical judge, who defeated a large force with a tiny band. Wingate invited a number of veterans of the Haganah SNS to join him. With the blessing of the Emperor of Ethiopia, Haile Selassie, the group began to operate in February 1941. During the Italian occupation of Ethiopia between 1936–41, the Italians waged operations to "pacify" Ethiopia that killed about 7% of the Ethiopian population. Given this background, there was huge reservoir of hatred for the Italians, and many Ethiopians were more than willing to assist Gideon Force. Temporarily promoted to Lieutenant Colonel, Wingate was put in command. He again insisted on leading from the front, accompanied his troops in the reconquest of Abyssinia. Gideon Force, with the aid of local resistance fighters, harassed Italian forts and their supply lines while regular army units took on the main Italian army. A small force of no more than 1,700 men took the surrender of about 20,000 Italians toward the end of the campaign. At the end of the fighting, Wingate and the men of the Gideon Force linked with the force of Lt. Gen. Alan Cunningham which had advanced from Kenya in the south and accompanied the emperor in his triumphant return to Addis Ababa that May. Wingate was mentioned in dispatches in April 1941 and was awarded a second DSO in December.

With the end of the East African Campaign on 4 June 1941, Wingate was removed from command of the now-dismantled Gideon Force and his rank reduced to that of major. During the campaign, he was irritated that British authorities ignored a request for decorations for his men. They obstructed his efforts to obtain back pay and other compensation. He left for Cairo and wrote an official report which was extremely critical of his commanders, fellow officers, government officials and many others. Wingate was also angry that his efforts had not been praised by authorities and that he had been forced to leave Abyssinia without having said farewell to Emperor Selassie. He was most concerned about British attempts to stifle Ethiopian freedom, writing that attempts to raise future rebellions amongst populations must be honest ones and should appeal to justice.

Although there are contrary views about Maj. Gen. Wingate, General Wavell, now Commander-in-Chief in India, commanding the South-East Asian Theatre was asked if there was any chance of employing Wingate in the Far East. On 27 February 1942, Wingate, far from pleased with his posting as a "supernumary major without staff grading", left Britain for Rangoon, Burma.

On Wingate's arrival in March 1942 in the Far East, he was appointed colonel once more by General Wavell, and was ordered to organise guerrilla units to fight behind Japanese lines. However, the precipitous collapse of Allied defences in Burma forestalled further planning, and Wingate flew back to India in April, where he began to promote his ideas for jungle long-range penetration units. "Never ask favours", he recalled from his long association with Wavell, "but tell people if they care to help they can come along, that you yourself are going anyway."

Intrigued by Wingate's theories, Wavell gave his old friend a brigade of troops, the (Indian 77th Infantry Brigade), from which he created a jungle long-range penetration unit. 77 Brigade was eventually named the Chindits, a corrupted version of the name of a mythical Burmese lion, the chinthe. By August 1942, he had set up a training centre at Dhana near Saugor district in Madhya Pradesh, India, and attempted to toughen up the men by having them camp in the Indian jungle during the rainy season. This proved disastrous, as the result was a very high sick rate among the men. In one battalion, 70% of the men went absent from duty due to illness.