Daniela Greene, who had 'top secret' security clearance, told colleagues at the Detroit FBI office that she was travelling to Germany to see her parents for a few weeks in June 2014.
Instead, she flew to Turkey and crossed the border to meet up and marry the IS fighter, identified in reports as Denis Cuspert - a German former rapper who went by the name Deso Dogg.
Cuspert was officially designated a terrorist in 2015 by the US State Department, and is described as an IS recruiter who has targeted German speakers and has appeared in a number of the extremist group's videos - including one in which he holds a severed head.
It is unclear how Cuspert, also known as Abu Talha al Almani, began the relationship with Greene.
Court testimony suggests they may have communicated privately using a Skype account that Greene did not report to her FBI colleagues.
Greene, 38, was born in Czechoslovakia and married a US soldier. She began working at the FBI in 2011 and had no issues on her record until her disappearance three years later.
She married Cuspert on 27 June 2014, immediately after arriving in Syria, according to recently unsealed court documents.
But within days she began to seek a way out of the marriage.
In an email to a friend in July 2014, she wrote: "I really made a mess of things this time."
In a later email she said: "I don't know how long I will last here, but it doesn't matter, it's all a little too late."
She also wrote that she recognised she could be imprisoned for years if she returned to the US.
It was unclear how she escaped from IS territory, but she returned to the US in August and was arrested.
She immediately confessed and co-operated with US prosecutors. She subsequently pleaded guilty to one charge of "making false statements involving international terrorism".
She was jailed for 24 months and was released last year, the court documents show.