The left-back has been handed a one-match suspension by the FA for his sending off against Sunderland on November 4.
Thatcher was shown two yellow cards for dissent by referee Dermot Gallagher and bans are dished out two weeks after the incident - hence he's out for the televised clash.
It leaves manager George Graham in a bit of a quandary with natural replacement Mauricio Taricco still recovering from a groin injury.
Luke Young would be a possible replacement but he has been playing in a sweeper's role recently as George adopts a five-man defensive system in the absence of Sol Campbell - who faces another fortnight out.
Stephen Clemence filled the vacancy in Taricco's absence last season but he is still needed in midfield with both Oyvind Leonhardsen and Steffen Freund crocked.
It could mean an appearance for youngsters Ledley King - who made his debut at a left-back against Liverpool at Anfield in 1999 - or Alton Thelwell, who has been a regular on the bench in recent weeks.
Ben Thatcher is suspended for Sunday's visit of Liverpool.