In the summer of 1943, after his first year of college at Harvard, Allen H. Meyer began studying Japanese privately at the University of Chicago. He had already studied six other languages, and in the fall he entered a civilian Japanese program at Ann Arbor, Michigan. In early 1944, the Army drafted him and he attended infantry basic training at Camp Roberts, but had already received recognition for his adept language ability.
Capt. Kai Rasmussen, one of the Military Intelligence Service Language School (MISLS) administrators, pulled Meyer out of basic training and sent him back to classes at Ann Arbro as a private. After Meyer graduated from that program, Meyer went to MISLS at Fort Snelling, Minn., for additional training.
In his first assignment after graduation, Meyer went to Tokyo, Japan, to work for the Allied Translator and Interpreter Section (ATIS) in the periodical section:

> We were mainly concerned with the treatment of matters such as possible war criminals (whose actions might be undemocratic), breaking up the zaibatsu [the financial clique that controlled the government], the role of women, and labor and management. [Autobiography]

While they translated the documents, Meyer often had discussions with other linguists about the nuances in their translation work, which created an excellent chance for engaging cross-cultural learning. Those discussions also sparked larger discussions on the changes the Occupations was brining to Japan, and even after his assignment at ATIS ended, Meyer would often visit his colleagues.
Although not considered "official" work, he often traveled with military officers to parties and other social events to act as a guide and once helped calm disturbances between Occupation Military Police and homeless Japanese. With his free time, Meyer would travel around Honshu, Japan's largest island, by jeep or by local trains and practiced his Japanese with people he met through his travels.
In March 1946, he moved to Uraga where many Japanese soldiers were returning from Southeast Asia and the East Indies. With a team of other linguists, he accepted the soldiers' surrenders and debriefed them as they returned. When Japanese prisoners of war began returning from Manchuria and Siberia, Meyer interrogated the returnees before they were allowed back into Japan. With hundreds of other repatriates watching them, he and the other linguists would talk to Japanese repatriates before allowing them into the country:

> Our basic concern always had to be with the impression we left on these people before they returned home.... Considering the lack of privacy, and the fact that we were being observed by hundreds of others at a distance, an appearance of not being overbearing was essential. [Article]

On one ship returning from the East Indies, more than 8,000 soldiers, still armed, entered Uraga Bay. Meyer boarded the ship with a team of five men and successfully won the cooperation of the ship's general and all of the officers. In another incident, a ship from Europe full of Japanese diplomats came and expected special treatment. When Meyer asked them to open their trunks, they ignored him and spit epithets at the soldiers who forced their luggage open. Later, the evidence taken from the trunks was used in the war crimes trials.
In April 1947, Meyer received orders to survey and watch over the second round of elections in Hokkaido, Japan. The first elections, held in 1946, had not gone well, and the Occupation forces hoped that this election would speed Japan's progress toward a representative democracy. With a team of linguists Meyer trekked through drifts of snow 20 feet high, visiting polling and ballot-counting places to make sure the process went smoothly. For the most part, the Japanese appreciated his team's interest in their country's early attempts at open elections. In a letter he wrote home to his family, Meyer recounts his work:

> Today, counting day, gave us a very satisfied feeling. This election was for the members of the local village, town and city assemblies, and the Hokkaido Assembly, and the people knew much more about the candidates and, therefore, showed much greater interest in the entire affair.... In one place, over 150 people stood for three hours to watch the "democratic" way an election should be handled, and seemed to enjoy every minute of it. When we arrived they seemed rather pleased at seeing us, for it probably gave them a certain feeling of thankfulness that we showed such a great interest in their election.... The end of a very interesting venture--another phase in the democratization of Japan. ["Translator/Interpreter"]

In September 1947, Meyer returned to the United States to complete his degree at Harvard. Then, in 1951 he earned a law degree.