In a 6-3 opinion, the Supreme Court ruled in favor of the United States. Justice Black wrote the majority opinion. The majority concluded that the President and Congress did not act outside of their constitutional authority, and that the exclusion order did not violate the 14th Amendment. Justice Murphy dissented, arguing that the exclusion order was primarily based on racism. Justice Jackson and Justice Roberts also dissented.

The justices in the majority compared the case to Hirabayashi v. United States (1943), a previous case in which the Court had upheld a military order imposing a curfew on people of Japanese ancestry living on the West Coast. In that case, the Court concluded that the curfew order was within the war powers of Congress and within the authority of the President as Commander in Chief because its purpose was to further the national defense during wartime by preventing espionage and sabotage. The exclusion order at issue in Korematsu was justified in the same way. Because the exclusion order was issued during wartime, the Court gave great deference to the judgment of military authorities, Congress, and the President, all of whom deemed the measure necessary. The justices concluded that the Court “[could] not say that the war-making branches of the Government did not have ground for believing that in a critical hour such persons … constituted a menace to the national defense and safety.” According to this reasoning, the power of Congress and the President are greatly expanded during wartime, in which “the power to protect must be commensurate with the threatened danger.”  

The Court decided that the exclusion order did not violate the equal protection clause of the 14th Amendment.  While the justices acknowledged that “all legal restrictions which curtail the civil rights of a single racial group are immediately suspect,” they determined that all such restrictions were not necessarily unconstitutional. The Court ruled that even though the exclusion order only targeted a specific racial group, it was not based on hostility towards those of Japanese ancestry.  Rather, it was because military authorities did not have the time or resources to efficiently separate those who were disloyal from those who were loyal that all people of Japanese ancestry as a group were subject to the exclusion order. If the exclusion order had been based solely on racial prejudice, however, it would be unquestionably unconstitutional.

Justice Murphy wrote a strongly worded dissent. Calling the exclusion order “the legalization of racism,” he believed that it violated the equal protection clause of the 14th Amendment. He acknowledged that in wartime, military authorities must be given great deference as those best equipped to make decisions to protect the security of the nation, but he argued that military decisions must still be subject to judicial oversight. Measures deemed necessary by military authorities must be reasonably related to preventing invasion, sabotage or espionage. According to Justice Jackson, that standard was not met here because there was no evidence proving that people of Japanese ancestry living on the West Coast were a threat to the safety of the United States. Instead, the decision to force them into internment camps was based on “an accumulation of much of the misinformation, half-truths and insinuations” that had long been the source of racial prejudice against Japanese Americans. He compared the exclusion order to the “abhorrent and despicable treatment of minority groups by the dictatorial tyrannies which this nation is now pledged to destroy,” and concluded that the exclusion order violated the 14th Amendment by “fall[ing] into the ugly abyss of racism.”