After the Army adopted an enlisted man's shirt with a full frontal opening (Olive Drab Coat Style Flannel Shirt, Specification 8-26C dated 4 October 1933), the next major design change saw the approval of a sports style shirt offering the soldier greater practicality and comfort. Re-design of the shirt into a sports style came about through repeated attempts during the late 1930's and early 1940's to develop a suitable khaki cotton shirt for wear in hot and tropical climates. The new shirt would feature a convertible collar
The sports or convertible collar allowed a shirt to be worn open at the throat while maintaining a neat appearance. This effect was made possible by increasing the distance between the collar button and the first button below it, thereby allowing the collar to lay flat when unbuttoned. and a new front facing, which eliminated the dress style collar and placket band of the old shirt. These changes allowed the shirt to be worn open collar in hot weather and field conditions, or with a necktie when regulations required. A single specification was issued for the new sports design that included both cotton and flannel shirts (Khaki Cotton Shirt and Coat Style Olive Drab Flannel Shirt, Specification PQD 96A dated 8 October 1941). Issuing a single specification for both shirts enabled manufacturers to produce either type without needing to change their plant equipment or assembly process. This practice helped the Army prepare for and meet increased production demands in times of emergency.

Though the basic design was set, the flannel shirt would see several changes throughout the war years. During March 1942, special gas protection features were added in the form of a flap behind the front closure, gusset-like pieces of material behind the cuff openings, and two buttons behind the collar for attaching a hood. The hood (Special Olive Drab Wool Hood, Specification PQD 90B dated 10 April 1942) was to be used in conjunction with the issue gas mask. Protective features were added to many types of clothing items at this time because it was decided it would be more efficient to add them to existing designs rather than develop specialized garments. The updated flannel shirt was identified by the addition of "special" in the nomenclature wording and through a new series of stock numbers that differentiated it from the old.

The cuff design was changed in 1942 and again in 1943. In 1942 the piece of material that had been added behind the cuff opening for gas protection was eliminated. To allow for this change and still protect the wearer, the length of the sleeve opening was sewn shut to the top of the cuff, thereby eliminating the need for the extra material (Specification PQD 96C, dated 23 June 1942). This design did not prove practical, however, and the cuff was again changed in 1943. This time, the piece of material used for gas protection was returned to its position behind the cuff, but the finish of the cuff was changed from a refined shirt-style
The shirt-style cuff, shown on the left, was finished with a placket. In the spring of 1943 the cuff design was changed to the lapped style, shown on the right, and used to the end of the war. to a simplified lapped style (Special Coat Style Olive Drab Flannel Shirt, Specification PQD 96D dated 21 April 1943). The flannel shirt pattern drawn up in April 1943 would continue to be used through the end of the war. This shirt, most identified with the war years, became the most ubiquitous pattern type. It is easily recognized by its lapped cuffs, convertible collar, sports front, and gas protection features.

In 1944 the practice of issuing a single specification for the enlisted man's shirt ended. This was due to an authorization for significant changes that were to be made to the khaki shirt in order to conserve cotton material. Thus, the flannel and cotton shirts were made under separate specifications for the first time since early 1942 (Special Coat Style Olive Drab Flannel Shirt, Specification PQD 473 dated 4 November 1944; and Khaki Cotton Shirt, Specification 475 dated 6 November 1944). The newly designated flannel shirt retained its previous design features and continued to be produced using the pattern of 21 April 1943.

The specification 473 wool shirt was not entirely without change, however. During this time the shirting flannel and buttons were shifted to a darker color. In the spring of 1944 the color of the woolen trousers had been changed to a darker shade of olive drab while being redesigned and upgraded for more effective field wear. So, when flannel shirt production resumed in December 1944, the changeover to a darker shade of material occurred (point here for color comparison).
Pictured on the left is the Special Coat Style Olive Drab Flannel shirt, specification 96D, dated 21 April 1943, manufactured in "light shade" or sometimes referred to as "mustard" color. Prior to 1944, flannel shirts and service trousers were manufactured in a "light shade" of olive drab providing a color contrast to the darker service coat. In 1944 woolen trousers and shirts were darkened to provide better camouflage properties when worn in the field. On the right, for relative color reference, is the Special Coat Style Flannel Shirt, specification 473, of 1944. The new material would bring the flannel shirt into conformity with the other new woolen field uniform components (Olive Drab Wool Field Jacket, Spec. PQD 437 dated 12 May 1944; and Special 18 oz Olive Drab 33 Serge Wool Field Trousers, Spec. PQD 353B dated 21 November 1944). Old stocks of light shade shirting flannel continued to be used up during the conversion period. This practice resulted in some specification 473 shirts being fabricated utilizing the new dark color buttons combined with surplus light shade flannel. The vast bulk of flannel shirts produced from December 1944 onward were, however, made up in the darker flannel.

Some late war examples of the enlisted man's flannel shirt had "GAS FLAP" boldly ink stamped on the gas flap appendage. This, presumably, was to help prevent soldiers from cutting the flap out. It is quite common to find surviving examples of special coat style flannel shirts that have had their gas flaps removed.

After the war ended there was a very brief production of convertible collar, sports-style shirts without the gas protection features. Shortly thereafter, though, the enlisted man's flannel shirt returned to its pre-war dress style design. In the spring of 1946, the flannel shirt regained its stand-up collar and front button placard. At this time shoulder loops were also added to the shirt.