Centre-back Flaherty, 22, was recently included in new England manager Mark Sampson's first squad, while central midfielder Katie Chapman has represented her country on more than 80 occasions.
Both players have signed from Women's Super League rivals Arsenal Ladies having helped the Gunners to multiple league and cup honours during their time at the club.
Chelsea Ladies manager Emma Hayes, who worked with both Chapman and Flaherty during her time as Arsenal Ladies assistant manager, said: 'Gilly is the best uncapped player in the country. In my opinion she will become a bedrock for club and country as she has all the hallmarks of a top class player.
'Katie is best at what she does in this country and I am sure any manager in the country would say the same. Her experience and winning mentality is what sets her apart and she is a fabulous role model too.'
Flaherty added: 'I'm delighted to join Chelsea and am really looking forward to a new challenge. It was a really tough decision to leave Arsenal but getting the chance to work with Emma again plus the vision here at Chelsea was just too good to turn down.
'The ambition of the club matched mine, I'm a winner and I'm determined to win trophies for the club and compete to play for England in major tournaments in the near future.'
Chelsea Ladies completed the signings of England pair Rachel Williams and Laura Bassett from Birmingham City Ladies in November, with the duo helping Hayes' team to the final of the International Women's Club Championship in Japan in December.
The new Women's Super League season kicks off in April and Chapman can't wait for the action to get underway.
'I am delighted to be here and it is an exciting new chapter in my career,' said Chapman, who began her career with Millwall and has also played for Chicago Red Stars.
'Chelsea is a massive club with a big-club mentality so it is a new challenge for me, which is exciting. The staff and the players are really ambitious here so for me to be part of that is something I am over the moon with.'