On 17 June 1940, five days before the signing of the Franco-German Armistice, the first "exodus" (of 10 airmen) took flight from Bordeaux-Mérignac to England. Others rallied to General Charles de Gaulle from France and French North Africa during the period June 1940 to November 1942. A contingent of volunteers from South American countries such as Uruguay, Argentina and Chile was also created, as Free French officials recruited there personally. From a strength of 500 on July 1940, the ranks of the FAFL grew to 900 by 1941, including 200 flyers. A total of 276 of these flyers were stationed in England, and 604 were stationed in overseas theaters of operation. In the summer of 1940 General de Gaulle named then-Colonel Martial Henri Valin as commander-in-chief of the FAFL. Valin was at the French military mission in Rio de Janeiro, Brazil at the time of his appointment and he had to complete his assignment there by February 1941. It took him 45 days to get to London to see de Gaulle and it was not until 9 July that Valin formally assumed office taking over from the caretaker commander, Admiral Emile Muselier.
All FAFL aircraft were to be identified differently from those of the Vichy French air force, which continued to use the pre-war tricolor roundel. In order to distinguish their allegiance from that of Vichy France, the Cross of Lorraine - a cross with two parallel horizontal arms, with the lower arm slightly longer than the upper one - was the symbol of Free France chosen by Charles de Gaulle. The cross could be seen in the same places on FAFL aircraft where the roundels used to be on all French military aircraft, that is, on the fuselage and on the lower and upper surfaces of the wings. The FAFL was formed with one “mixed” unit at RAF Odiham on August 29, 1940, under the command of Commandant (Major) Lionel de Marmier. One of its first jobs was to try to persuade the governors-general of colonies in French West Africa not to submit to the orders of the Vichy government, and instead join the Free French in their continuing fight against the Axis Powers of Germany and Italy.
Operation Menace was the Allied plan to take persuade Dakar (as de Gaulle believed was possible) to join the Allied cause, or capture it by force. Among the units taking part was the newly formed FAFL Groupe de Combat Mixte (GMC) 1, code-named "Jam", consisted of four squadrons, composed of Bristol Blenheim bombers and Westland Lysander liaison/observation aircraft. The resulting Battle of Dakar was a failure. The port remained in Vichy control, FAFL envoys were arrested and imprisoned at Dakar by the Vichy authorities, and de Gaulle's standing was damaged.
However, French forces in Cameroon and Chad, in French Equatorial Africa, rallied to the Gaullist cause. There were three detachments of French air force units — based at Fort-Lamy (now N’Djamena) (Chad), Douala (Cameroon) and Pointe-Noire (Congo) – operating a mixed bag of Potez and Bloch aircraft, and they thus became part of the FAFL. However, Gabon remained loyal to Vichy, so, in mid- to late October 1940, FAFL squadrons set out on photo-reconnaissance and leaflet-dropping missions. The first combats between Vichy and the FAFL took place on 6 November 1940, when two Vichy air force aircraft took on two FAFL Lysanders near Libreville. Both aircraft sustained damage but made it back to base. Two days later, the first FAFL airmen were shot down and taken prisoner. Two days after that, Libreville was taken by Free French army troops, resulting in the FAFL aircraft now operating from the air base that had been used by their opponents of a few days before. The French attitude towards the fighting was that of a “civil war” that was being won for Free France, since now Libreville had joined the Gaullist cause. As it happened, this would be the only time when opposing factions within FEA territory would fight each other openly.
Philippe de Hauteclocque, better known by his French resistance name of "Leclerc", who later became one of the most famous French army generals in history, had strong ambitions in North Africa. But in outlining what he wanted the FAFL to do, he often revealed a complete lack of understanding of what it was actually capable of. When he demanded that the Italian-held airfield at Koufra in Libya was to be bombed, he was told, matter-of-factly, that the squadrons had no capability of carrying out such a major mission, especially given the lack of experience in navigating over vast desert territory. Leclerc’s reaction, based on his fury at lack of air support during the German invasion of France, was ugly, and relations between him and the FAFL deteriorated rapidly. A mission carried out by the recently formed Groupe de Bombardement (GRB) 1 (Lorraine) on February 4, 1941, ended disastrously when, out of four Blenheims sent to bomb Koufra, only a single one returned – and, even then, it was because of engine trouble. (It was not until 1959 that one of the other three aircraft was found.) On February 27, the Free French took Koufra airfield, while the enemy garrison surrendered two days afterwards. Leclerc, for his part, still regarded aviation as a kind of appendage, of such minor importance that it might as well not be there to support the ground forces at all.