More than 150 law enforcement officials had been searching for Jakubowski, 32, since April 4 when authorities say he broke into a gun store in Janesville, about 70 miles (110 kilometres) southwest of Milwaukee.
According to authorities in Vernon, Richland and Rock Counties, the Vernon County Sheriff's Office received a report of someone suspicious on a farmer's property on Estes Road near Readstown, Wisconsin at 9:30 p.m. Thursday.
Communities in Rock County - and really across Wisconsin - were on edge since news of the manhunt for Joseph Jakubowski got out.
Jakubowski was taken into custody shortly after 6 a.m.
Joseph Bugni, Jakubowski's appointed attorney, was surprised to learn his client was being held in Rock County where he also has been charged with burglary, theft and possession of burglary tools.
Jakubowski is suspected of stealing an arsenal of weapons from a gun store in southern Wisconsin and of mailing a threatening manifesto to the White House.
The FBI says there are no additional threats related to the fugitive who was arrested in southwestern Wisconsin following a nine-day manhunt.More news: Asian stocks slip, yen and gold rise as global risks weigh
Janesville Police Chief David Moore earlier said Jakubowski cited concerns about President Donald Trump in his 161-page manifesto, but that he didn't make any specific threats. But the suspect has not been a fan of authority, especially police officers, since age 17, he said.
An unnamed associate recorded Jakubowski mailing the manifesto on the afternoon of April 4.
CAPTURED! Awesome work to the men and women who worked this case.
"The full scale of (Jakubowski's) actions are under review", Tolomeo said.
WTMJ also reported that in the manifesto "Jakubowski refers to health insurance, taxes and religion as examples of the government trying to brainwash its citizens". Following the arrest, Gov. Scott Walker thanked authorities on Twitter. Investigators have two copies of the manifesto: the original mailed to Trump; and a version provided by a cooperating source.
Authorities said Thursday they had no information to suggest the fugitive was getting help to evade capture. "It's like a huge weigh is lifted", said Joni Bozart, store owner, Janesville. The tips largely came from local and state residents, with a few originating as far away as Texas and Oklahoma, they said.