Wigan teenager Nicholls has been a big success for the Cobblers since linking up with the npower League Two club at the start of the season. However, he returned to the DW Stadium this week after that initial deal expired.
Boothroyd is adamant he will be able to keep the player and he hopes to have him available against Bradford in the FA Cup first round on Saturday.
"He is staying. All being well all we have got to do is dot the Is and cross the Ts," said Boothroyd at his pre-match press conference on Thursday.
"These loan agreements can be painstaking because the parent club wants to make sure that their house is in order because they don't want to lose a player, particularly in the windows they work in, if they can't potentially call their players back.
"But I fully expect Lee Nicholls to be back with us by the close of play this week. However, [his availability for Saturday] it is one of those things that we need to iron out."