Rami Abdurrahman says the hacking will not deter him from reporting on the violations carried out by all parties in the Syrian conflict.
The Observatory, which has been tracking Syria's conflict since it started in March 2011, has been aggressively reporting over the past year on atrocities committed by the Islamic State extremists.
The group's website was not opening on Wednesday afternoon.
Abdurrahman says the hackers put a photo-shopped photograph of him on the webpage. It shows him wearing an orange jumpsuit while a masked man in black stands behind him with a knife something reminiscent of beheading photographs published by the IS in the past.