Federal Judge Richard Kopf ruled that the state could carry out the execution, its first in 21 years, using a four-drug protocol.
Fresenius Kabi had argued it was the likely source of two of those drugs, and their use in an execution would hurt the company's reputation, especially with a European public largely opposed to capital punishment.
The German group argued that it had protocols in place to prevent its drugs from being obtained by state agencies for executions, and that if Nebraska had purchased the drugmaker's injectable medicines, it had done so improperly.
But Kopf rejected the company's arguments, issuing an oral ruling from the bench saying that since Nebraska has not publicly identified the source of its execution drugs, the company's concerns were too speculative.
Fresenius Kabi reportedly planned to appeal the ruling, which for the time being did not alter the planned execution date of convicted murderer Carey Dean Moore, set for Tuesday.
Moore was sentenced to death for the 1979 murder of two taxi drivers. He is not contesting his execution order, but it could nevertheless be delayed by the lawsuit, should it prevail in an appeal.
“Decades have slipped by since Mr Moore was sentenced to death. The people of Nebraska have spoken,” the judge said in his ruling.
“Any delay now is tantamount to nullifying Nebraska law, particularly given the rapidly approaching expiration of two of the drugs and the total absence of any feasible alternatives.”
State officials have said they obtained the drugs legally, although they have kept their source secret.
Injectable drugs have become harder to obtain amid public opposition and a reluctance or refusal by drug manufacturers to sell their products to prisons for use in executions.
Last month, a similar lawsuit by drugmaker Alvogen temporarily halted an execution in Nevada.