Boston's 10-point deduction will apply to this season's tally, the Football League has confirmed.
The club's Company Voluntary Arrangement was activated in the final seconds of their League Two defeat at Wrexham, which saw them relegated.
That led to uncertainty over whether the 10 points would be deducted this season or next season.
But a league statement confirmed: "Boston have been deducted 10 points from their points tally for 2006/07."
It added: "This Sporting Sanction takes effect from April 25th, the date on which the club effectively obtained the approval of creditors for a Company Voluntary Arrangement."