Steve Williams, the British ambassador to Bulgaria, was appointed on Tuesday and will take up the post in April.
Both islands agreed to set up a Brussels office last year, to ensure their interests were represented in the European Union.
Mr Williams said he has a lot to learn ahead of taking up his new job.
He said: "I'll be very keen to spend some quality time on the islands to get to know people, to get to know the issues.
"Once the office is up and running properly and I'm established it will be really important to come back regularly."
Guernsey's Chief Minister Lyndon Trott described the role of the office as "vital" in how the Channel Islands "engage with Brussels and the European Union over the coming years".
The appointment of a deputy director to assist Mr Williams in his new role is expected to be announced shortly.
The man chosen to head up the Channel Islands' new Brussels office has admitted he has little first hand knowledge of the islands.