A federal judge Monday denied the administration’s request to hit pause on a House lawsuit over Obamacare so that it could appeal an earlier, and notable, ruling that allowed the case proceed in the first place.

U.S. District Court Judge Rosemary M. Collyer enthused conservatives and shocked Democrats last month by granting House Republicans legal standing to sue President Obama, after lawmakers said his administration continued to dole out cost-sharing payments under the Affordable Care Act even though lawmakers had not approved them.

On Monday, the same judge prevented the Justice Department from appealing that decision before she can move on to the merits of the case.

Judge Collyer, appointed by President George W. Bush, said allowing the administration to plead its case to the appellate courts now would not terminate the case any faster — one of three key factors she had to weigh — because she is set to deliver summary judgment after a few months of briefing and oral argument.

“The relevant question is whether immediate appeal would materially advance the ultimate termination of the litigation. In this case, it would not,” she said in a written order.

House Speaker John A. Boehner, the Ohio Republican who plans to step down once Republicans choose someone to replace him, swiftly cheered the ruling.

“The court has previously ruled that the House does, in fact, have standing to challenge one of the president’s unilateral actions with regard to Obamacare,” he said. “Today’s ruling further underscores that point, and ensures that the District Court will hear the merits of the case this fall.”

Judge Collyer set out a briefing schedule that brings the parties into January, at which point she will schedule oral argument.

The case stems from a lawsuit filed last November that challenged Mr. Obama’s moves to twice delay the health law’s insurance mandate on employers, and to reimburse insurers who have reduced co-pays and deductibles for qualified Obamacare enrollees as a condition of participating in the state-based health care exchanges.

Republicans said Congress never authorized the reimbursement money, and indeed specifically rejected an administration request for that spending, so by moving ahead anyway Mr. Obama violated Congress’s constitutional power of the purse.

If the House succeeds on the substance of their suit and inevitable appeals, it would spell trouble for Mr. Obama’s namesake law. Nearly 6 million Obamacare customers with incomes between 100 percent and 250 percent of poverty rely on the payments, according to recent analysis by Avalere Health, a D.C.-based consultancy.

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