Cox suffered severe brain injuries when he was attacked by a group of AS Roma supporters prior to a UEFA Champions League semi-final game at Anfield in April 2018.
The 54-year-old received treatment in the Republic of Ireland for 18 months before moving to a neurological facility in England to begin a 12-week rehabilitation programme aimed at developing his speech and movement.
"This is a day we as a family have been looking forward to for a long time," Cox’s wife, Martina, wrote in a Facebook post.
"While Sean still has a long road to travel, having him home with us is an incredibly important step as we come together as a family unit again.
"I can't thank enough those who have helped Sean along the way over the past two years. Without a doubt this support has made today possible.
"In particular, I would like to thank the incredible staff in Marymount Care Centre in Lucan for the care and support they have provided to Sean over the past number of months.
"At a time when staying at home takes on new meaning for all of us, it's clear that there is no other place that Sean would rather be."
In February last year, Italian fan Simone Mastrelli pleaded guilty to attacking Cox and was sentenced to three-and-a-half years in prison.
Cox returned to Anfield last November as a special guest of honour for the first time since the attack to watch Liverpool defeat Manchester City 3-1 in a Premier League game.