Redknapp, who is on trial for tax evasion, which he denies, has been in court and has missed training since Monday but will still be at the match on Friday evening, his assistant manager Kevin Bond said on Thursday.
Bond told reporters at the club's training ground at Chigwell, north of London, that Redknapp's absence is having "very little" effect on preparations for the match.
He said that Redknapp had been in daily contact with both him and first-team coach Joe Jordan about the cup clash talking before and after training every day.
"Yes, he will be at the match and yes, he will pick the team," Bond said on Thursday.
"The fact that the manager has not been here has had very little impact. Harry will have a look at who's fresh and who's available - we've got one or two knocks."
Redknapp was also absent earlier in the season when he was in hospital for minor heart surgery.
"Its a similar scenario to when Harry had a small medical procedure. We didn't have him for a week or so leading up to the Fulham game," Bond said.
"The training carries on as normal, so there's not a lot of difference except that Harry's not here in the day."
"We haven't had a chance to discuss the team in great depth. There's also a game four days after the match against Wigan at home that we have to consider."
Tottenham, who are third in the Premier League with just two defeats in their last 20 league matches, start as strong favourites to beat Watford, who are 18th in the Championship.
Spurs have won all four matches they have played against Watford in the FA Cup, including a 4-1 win in the 1987 semi-final at Villa Park and a 5-2 win the last time they met in the competition in a third round match in 1999.
