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Bolger, 22, who had a loan spell with the club last season, has signed a two-year deal with the option of a third.
The defender, who joined the club from Leicester City in January 2013, featured heavily for the Whites' development and under-21 squads during the course of the 2013/14 campaign and was also captain of the side, however he failed to break through and make his first team debut.
Since his arrival in 2013 Bolger has enjoyed various loan spells to Colchester United and more recently Southend United. However, when Bolger joined League Two side Southend United on a 28-day loan his loan spell was cut short after just one appearance due to an ankle injury on 24 February 2014.
He will now join up with former Whites player and assistant manager, Phil Brown, at Roots Hall. The club's official website reported that Bolger had joined on an undisclosed fee, however the transfer fee is believed to be in the region of £25,000, substantially less than what was paid for his services in 2013.
Despite the low fee, it has been reported that there has been a sell-on-fee clause included in Bolger's move to Southend United.
Speaking to Southend's official website this is what United's manager, Phil Brown, had to say about the transfer:
"I can't emphasise enough how much this deal means to me as the manager of this football club.
"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."
Phil Brown's side start their season with a trip to Accrington Stanley on Saturday.
Later on in the interview on the club's official website, this is what Bolger had to say about his new club,
"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.
"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."