After a trip to South America in January 1946, in which he developed a heart arrhythmia severe enough to cancel the remainder of the trip, Arnold left active duty in the AAF on February 28, 1946, (his official date of retirement was June 30, 1946).
Leta 1945 je Arnold omogočil ustanovitev Projekta RAND (poznejša Korporacija RAND) z 10 milijoni $ ustanovitvnega denarja, ki so ostali neporabljeni od druge svetovne vojne.