The 21-year-old only arrived at Roots Hall on Friday, joining on a month-long deal, but he picked up the injury during his Shrimpers debut in Saturday's goalless draw at York.
Southend boss Phil Brown told the club's official website: "We've not had much luck bringing in defensive loanees this season, having lost Luke O'Neill already after just one game.
"Luke has gone back to Burnley and will probably be out for eight to 10 weeks which is frustrating.
"Now Cian has also had to go back because of the ankle injury he picked up, and he could be out for just as long.
"It's frustrating because he did really well on Saturday, but took a knock to the head too with a cut just below his eye.
"There's not much we can do, but we thank him for his efforts on Saturday after spending just an hour with his team-mates.
"We may have another look in the loan market, but we've got the players in the dressing room who need to step up."
- Sports & Recreation