In 1917 Fleischer made the rank of captain.
In 1919-1923 he was the Staff officer of the Norwegian 6th division before becoming Commanding Officer of Infantry Regiment 14 (IR 14) in Mosjøen. While serving in North Norway Fleischer became an avid writer of military manuals and worked continually on developing the Norwegian Defence Forces in line with the special prerequisites caused by the Norwegian nature and society.
On 16 January 1939 he was made Major General (generalmajor) and Commanding Officer of the Norwegian 6th division, the position that would lead him to become the first allied general to defeat the Wehrmacht in a head-on land confrontation.
In 1940, as commander of the Norwegian 6th division, Maj. Gen. Carl Gustav Fleischer coordinated Norwegian, French, Polish and British forces in the recapturing of Narvik on May 28 from Maj. Gen. Eduard Dietl's Austro-German 3rd Mountain Division. This was the first major allied infantry victory in WWII. Unfortunately, after the German invasion of France and the Low Countries, launched on 10 May, 1940, the Allied task force was withdrawn in early June. Without the support from the Allies, the Norwegian Army alone was not able to defend its positions and the Germans recaptured Narvik on 9 June. After Norway's surrender, General Fleischer followed the King Haakon VII and the Norwegian government into exile in England as commander of the Norwegian exile army.
General Fleischer was known as an excellent and righteous officer and soldier who had been very critical of the Norwegian Labour Party's pacifist policies and razing of the Norwegian Army during the 1930s. The relative ease with which the Germans were able to execute Operation Weserübung proved he had been fatally right. Most likely because of a personal antagonism due to this fact, General Fleischer was bypassed when the exile socialist government of prime minister Johan Nygaardsvold decided to recreate the post of commander-in-chief of the Royal Norwegian Armed Forces. This post had existed temporarily during the 1940 campaign, but General Otto Ruge, who had been commander-in-chief during the campaign, stayed in Norway and surrendered with his troops. Instead of Fleischer, who was the obvious choice, the cabinet promoted the young Major Wilhelm von Tangen Hansteen directly to Lieutenant General and gave him the post.
During his exile in the United Kingdom, General Fleischer did an impressive job in building up a Norwegian brigade in Dumfries, Scotland. While stationed there, he received a number of allied awards. Among these were the Polish Virtuti Militari for bravery, the French Croix de guerre, and the British Knight Commander of "The Order of the Bath".
The cabinet ordered General Fleischer to take up a new post as commander of Norwegian forces in Canada. Apart from the Royal Norwegian Air Force's training base Little Norway near Toronto, which was already headed by Ole Reistad, there were no Norwegian forces in Canada. On 1 December, 1942, General Fleischer was ordered to the position of Military Attaché to Washington D.C. This was another obvious humiliation, since usually officers of the ranks of Major or Lieutenant-Colonel were serving in this position. Being too much for him to swallow, he shot himself with his own gun through the heart on 19 December, 1942.
Still disputed today, it is thought that one of the reason for sending him to Canada was because he favoured a series of coastal raids against Norway to hamper German use of the occupied nation. The prevailing view in the rest of the Cabinet was to build air and naval forces that could be used directly with Allied forces, as they feared such raids would provoke the Germans into severe punitive actions against the local populace, such as they did after the Telavåg incident.
When his ashes were brought back to Norway after the war, the Labour cabinet denied him a state funeral. Despite the presence of the King, the Crown Prince, and representatives of all other parts of Norwegian society, no representatives of cabinet or the Labour Party attended. When a monument to his honour was raised in Harstad at the headquarters of the 6th Division, with the presence of the King, the same thing happened.