Ionatan (his military documents give his name as Evnatan) Agaronov was born in 1921 in Baku, Azerbaijan, to a family of Juhuris (Mountain Jews), one of six children. In 1927-29, while the family lived in Qırmızı Qəsəbə (Kyrmyzy Kasaba) in northern Azerbaijan, Ionatan attended a Juhuri-language school and received religious instruction from a private melamed (religious teacher). In May 1940, he volunteered for the Red Army. Ionatan was assigned to a course for military translators in Baku, where, in addition to the common military training, he was to master Farsi, Turkish, and English. His second year of study was supposed to be devoted to reconnaissance, radio, and other matters related to military intelligence. However, in June 1941 the Soviet-German war broke out, and Agaronov was transferred to the Intelligence Department at the HQ of the Transcaucasian Front.
In August 1941, Agaronov took part in the Soviet invasion of Iran. Until summer 1942, he stayed in Tabriz, Iranian Azerbaijan. That summer, knowing that the enemy was advancing into the Caucasus, Agaronov requested to be transferred to the Intelligence Department of the Transcaucasian Front. In late 1942, the Soviet High Command received false intelligence about an alleged German incursion into Turkey. Agaronov was asked to check this information, and he was able to disprove it.
In 1943, Agaronov was posted back to Iran, to prepare for the meeting of the "Big Three" leaders (Franklin D. Roosevelt, Winston Churchill, and Joseph Stalin), which was to be held in November-December that year in Tehran.
In 1946, the Soviet forces withdrew from Iran, and Senior Lieutenant Agaronov was transferred to the Lənkəran (Lankaran) checkpoint at the Soviet (Azerbaijani) border with Iran. In 1948, Agaronov tried to enroll in the so-called "VAK" (Academy of Intelligence), but his application was denied, since Stalinist anti-Jewish policies were on the rise at the time. He went on to work in the financial and social institutions of the Transcaucasian Military District, and wrote texts in Farsi, Turkish, and Arabic for the Azerbaijani Broadcasting Agency. In 1979, he retired from the armed forces, having attained the rank of colonel.
In 1991, Ionatan Agaronov settled in Israel. He died in 2012