First flown in 1938, it used a Hispano-Suiza 12Y-31 V-12 engine, which gave it a top speed of 303 mph. The M.S.406 was armed with one 20 mm cannon and two 7.5 mm machine guns. Besides France, this aircraft was used by Croatia, Finland, Turkey and Switzerland.[N 1]
The M.S.406 was a direct development of the M.S.405, and was designed to incorporate all of the structural design and equipment changes that had been applied to individual examples of the earlier aircraft.
By the time of the British attack against the airfield at Palmyra on 14th May 1941, the 20 M.S.406s of G.C.I/7 based at Rayak were the only French fighters in the Levant area. 
Following heavy fighting in the Levant, the Vichy air forces received reinforcements in early July, including three M.S.406s.
On the morning of 12 July 1941, the day an armistice between the Vichy and British forces came into effect, a group of M.S.406s from G.C.I/7 attacked allied motor vehicles north of Raqqa, before being withdrawn to Greece. 
In February 1942, a Groupe Aerien Mixte was organised with two squadrons. One of these was Escadrille 565, equipped with 18 M.S.406s.
Received 36 examples in July 1943. These veterans of the Vichy France Air force, which were acquired to combat increased Allied air activity over the Balkans, were allocated to the newly formed 21st, 22nd and 23rd Jato of the 11th Group of the Croat Air Force. The Croat Air Force received a further 10 examples in December.
Received 30 examples, registered MS-301 to MS330, between 4th and 29th February 1940.  These aircraft were allocated to LeLv 28, commanded by Major Jusu.  Before the Armistice of March 1940, the M.S.406s carried out 259 sorties, resulting in 28 aerial encounters and the shooting down of 16 Soviet aircraft, for the loss of one M.S.406 and damage to three others. 
30 examples supplied during February and March 1940.
Supplied with a pair of M.S.406H aircraft - one in September 1938, the other in April 1939 - as pattern aircraft for a version to be built under license. These were hybrids combining the airframe of the earlier M.S.405 with the Hispano-Suiza 12Y-31 V-12 engine of the 406 and Swiss equipment. The resulting type was designated D-3800.
- Green, William and Gordon Swanborough. 2001. Page 418
- Gunston, Bill. Salamander. 1988. Page 12
- Neulen, Hans Werner. Crowood Press. 2000. Page 227
- Neulen, Hans Werner. Crowood Press. 2000. Page 232
- Neulen, Hans Werner. Crowood Press. 2000. Page 233
- Neulen, Hans Werner. Crowood Press. 2000. Page 179
- Neulen, Hans Werner. Crowood Press. 2000. Page 200
- Neulen, Hans Werner. Crowood Press. 2000. Page 201
- Neulen, Hans Werner. Crowood Press. 2000. Page 203
- Green, William and Gordon Swanborough. 2001. Page 419
- Green, William and Gordon Swanborough. Complete Book of Fighters. Salamander Books. 2001. ISBN 0-84065-269-1
- Gunston, Bill. Illustrated Directory of Fighting Aircraft of World War II. Salamander. 1988. ISBN 0-86101-390-5
- Neulen, Hans Werner. In The Skies of Europe - Air Forces allied to the Luftwaffe 1939-1945. Crowood Press. 2000. ISBN 1-86126-326-0