Late last week Vice-President elect Mike Pence was working with House Republicans to adopt a continuing resolution (CR) that would extend FY 2017 funding into the end of March of next year. Current funding for 11 of the 12 appropriations bills run out on December 9. The goal of a March extension is that the new Administration and the new 115th Congress can finish up spending decisions in a way more to their liking. The CR would likely provide flat funding with some slight adjustments to March.
Congressional Democrats have responded negatively to the proposal in both houses but it is unlikely they can stop such a decision unless the White House draws a line in the last weeks of the Obama Administration. There is some reluctance on the part of Senate Republicans but Majority Leader Mitch McConnell (R-KY) is likely to go along. A potential challenge for Senate Republicans is that they would be forced to deal with FY 2017 funding decisions early in January when they would like to focus on their new agenda. Senators will also have to deal with cabinet conformations, a possible Supreme Court nominee and efforts to repeal the ACA.
There are current challenges for funding for HHS. Both houses have wanted to provide increases in health research under the National Institutes of Health (NIH) but current bills have funded those increases with gimmicks or severe cuts in other areas. In all likelihood, a 115th Congress would shore up the rest of the FY 2017 budget by cutting from targets such as the ACA administrative and prevention funds as well as other political targets especially Planned Parenthood.