The actress was originally planning to helm the 14th instalment of the current season but later postponed in order to have a larger acting role in the two preceding episodes.
Deschanel recently told GiveMeMyRemote that she will now direct episode "20 or 21" of the show's sixth run.
"I'm supposed to direct the third-to-last or fourth-to-last episode of the season," she explained.
Her co-star David Boreneaz, who recently helmed the crime drama for the third time, previously admitted that directing the show is "challenging".
Bones airs on Thursdays at 8/7c on Fox.