Much of the money will be recouped now the government is open again but the CBO calculates $3bn will never be recovered and the full impact of the closure - which left hundreds of thousands of federal workers and contractors without pay - may be larger.
"Although their precise effects on economic output are uncertain", the CBO concluded, "those factors would have had increasingly negative effects if the partial shutdown had extended beyond five weeks".
The longest shutdown in U.S. history ended on Friday when Trump and Congress agreed to temporary government funding - without money for his wall.
A federal worker stands with a placard reading "Will Work For Pay" as other federal employees stage a rally to call for a vote on the shutdown on Capitol Hill in Washington, Jan. 23, 2019.
The partial shutdown of the federal government cost the USA economy $11 billion, according to analysis from the Congressional Budget Office (CBO), nearly double the $5.6 billion President Trump had requested for a border wall.
The estimates didn't incorporate more indirect effects of the shutdown, which the office said were more hard to quantify but were probably becoming more significant as it continued.
A substantial portion of GDP lost during the budget impasse is expected to be recovered, but roughly $3 billion will be lost forever, the CBO estimated. The shutdown, which ended last week, cost the economy $3 billion.
Anthem demo pre-loading is underway ahead of Friday's roll-out
Those looking to try out Anthem have a prime opportunity coming up, as EA is hosting a VIP demo for the game this coming weekend. While you can pre-install it now, the earliest you can begin playing is tomorrow Friday, January 25, but only if you are a VIP.
Trump said he would be willing to shut down the government again if lawmakers don't reach an acceptable deal, but on Sunday expressed skepticism that such an agreement could be reached.
Graphic shows the longest shutdowns in USA history.
Furloughed workers wait in line to receive food and supplies in Washington, on January 22. Though federal employees are expected to receive back pay, contracted employees likely will not.
Not only will compensation be affected, but so will tax revenues, CBO predicts.
The CBO said in the report that the "substantial reduction over the 10-year period is nearly entirely because appropriations for 2019 that are designated as emergency requirements total $2 billion so far - a sharp reduction from the $108 billion that was appropriated in 2018, mostly for relief and recovery efforts related to the hurricanes and wildfires that occurred in 2017".
"The shutdown dampened economic activity mainly because of the loss of furloughed federal workers' contribution to (gross domestic product), the delay in federal spending on goods and services, and the reduction in aggregate demand", the report said.