Congress and the president changed the government's status to "open" Thursday morning.
This allowed for the nation's debt limit to be temporarily raised until Jan. 15.
Hundreds of thousands of employees were back at their desks Thursday morning, including at the U.S. Department of Agriculture office in Columbia.
USDA and other federal employees told ABC 17 News they were happy to back, though they do have a lot of work ahead of them.
"I'm thrilled that we can offer full services now, which is wonderful," said Clay Hayden, district manager for the Social Security office.
The Social Security office was filled with people Thursday morning, finally able to change their names and discuss benefits.
The Head Start education program is awaiting word from the government to see if it will be refunded for the $20,000 spent on children's food during the shutdown.
"I think they are scrambling to get back to work and to figure out where their priorities are and what they've missed over the last 16 days. I think we'll hear very soon," said Darin Preis, executive director for Central Missouri Community Action.
Preis told ABC 17 News he expects to hear an answer by the end of next week.
The Social Security employees in Columbia who were on furlough will receive paychecks next week.
"I've just been really proud of my employees," said Clay Hayden, Social Security offices district manager. "We didn't pay them two weeks ago and they haven't been getting paid."