The ruling stems from a larger case in which Lehman sued to recover $11bn is assets to which it claimed Barclays wasn’t entitled.
In February, the court rejected most of Lehman’s claims but found that Barclay’s acquisition was not to include cash.
The UK bank said it would appeal against decision by James Peck, judge in the federal bankruptcy court in Manhattan.
Barclays is ordered by Judge Peck to hand over $2.1bn in funds. Since the Lehman trustee had agreed to return $1.1bn in other assets to Barclays, the ruling had the effect of requiring the UK bank to pay a net $1bn to the trustee.
However, Barclays lost its bid for $1.9bn in margin to offset liabilities it took on with some of the brokerage’s trading positions.
In a 103-page opinion Peck wrote "The court was not deceived in a manner that should now be permitted to upset the integrity of the sale order. The sale process may have been imperfect, but it was still adequate under the exceptional circumstances of Lehman Week."