The tie will take place at The Valley over the weekend of January 3rd/4th 2015.
Former Rovers favourite Alan Shearer picked out ball number five, to hand Rovers a trip to the capital early in the New Year.
The two teams, who face each other at Ewood Park in Rovers' next home outing on Saturday December 20th, last met in the competition in January 1999.
That day, Rovers ran out 2-0 winners thanks to goals at the end of each half from Kevin Davies and Jason Wilcox.
Rovers were knocked out of the competition at the third round stage last season, losing 5-0 to Manchester City at the Etihad Stadium in a replay after holding the current Premier League champions to a 1-1 draw at Ewood Park.
Rovers' trip to Charlton is one of six all-Championship ties, whilst the pick of the round - and first out of the hat - sees holders Arsenal host Hull City in a repeat of last year's final.
Third round draw in full:
Arsenal vs. Hull City
Southampton vs. Ipswich Town
Stoke City vs. Wrexham
Charlton Athletic vs. Blackburn Rovers
Dover Athletic vs. Crystal Palace
AFC Wimbledon vs. Liverpool
Manchester City vs. Sheffield Wednesday
Aldershot Town or Rochdale vs. Nottingham Forest
West Bromwich Albion vs. Gateshead
Blyth Spartans vs. Birmingham City
Aston Villa vs. Blackpool
Rotherham United vs. AFC Bournemouth
Huddersfield Town vs. Reading
Oxford United or Tranmere Rovers vs. Swansea City
Cardiff City vs. Colchester United
Bolton Wanderers vs. Wigan Athletic
Sunderland vs. Leeds United
Burnley vs. Tottenham Hotspur
Millwall vs. Bradford City
Derby County vs. Southport
Brentford vs. Brighton & Hove Albion
Fulham vs. Wolverhampton Wanderers
Leicester City vs. Newcastle United
Scunthorpe United or Worcester City vs. Chesterfield FC
Everton vs. West Ham United
Cambridge United or Mansfield Town vs. Bury or Luton Town
Chelsea vs. Watford
Barnsley or Chester FC vs. Middlesbrough
Queens Park Rangers vs. Sheffield United
Accrington Stanley or Yeovil Town vs. Manchester United
Preston North End vs. Norwich City
Doncaster Rovers vs. Bristol City