The Shrimpers brought in three new faces on Monday and have further strengthened by landing 6ft 3in 22-year-old Bolger on a two-year deal from the Championship outfit.
Bolger's loan spell at Roots Hall last term was cut short by an ankle injury, but Phil Brown is delighted to bring the former Leicester trainee back on board for a permanent stay.
"I can't emphasise enough how much this deal means to me as the manager of this football club," Brown told Southend's official website. "For the chairman to spend an undisclosed fee on a player who first appeared on the market two weeks ago for loan is a real statement of intent.
"To get a player of Cian's quality through the door is fantastic news - and with three arrivals on Monday, it really builds up the excitement ahead of the new season."
Bolger failed to make a first-team appearance for Bolton but was captain of their development squad and gained valuable experience in a season-long stint with Bristol Rovers a few years ago.
"I'm very pleased to have come back to Southend. My spell last time was very short, but I now have the opportunity to really settle down," Bolger commented.
"I felt it was time for me to make the permanent move instead of going on loan. It was a big decision, but I'm sure it will prove to be the right one."