Austin police Cmdr. Troy Officer said Wilson met the girl at a coffee shop on August 15 and later brought her to a hotel and paid her $500 for sex, according to CNN.
They say he flew to Taipei to evade the authorities.
The victim met Wilson on sugardaddymeet.com, a website that bills itself as the "Best Sugar Daddy Dating Site for Attractive Women and Wealthy Men Seeking Mutually Beneficial Relationships".
Wilson, who created blueprints for untraceable 3D-printed guns and posted them online, appeared in court in Houston after being deported from Taiwan, where he had fled after being told police were investigating allegations he had sex with the minor.
He was booked into Harris County jail in Houston on Sunday, according to the jail's website.
"This was a collaborative effort that demonstrates the dedication of local, state, federal and global officials working together to bring this fugitive to justice", U.S. Marshal for the Western District of Texas Susan Pamerleau said.
The girl told investigators that after having sex, he dropped her off at a Whataburger restaurant. And, in one message, "Sanjuro" identified himself as Cody Wilson, police said.
But multiple states filed a joint lawsuit claiming Wilson endangered public safety through his actions, and a federal judge issued a temporary order prohibiting the distribution of the digital blueprints.
The age of consent in Texas is 17.
He then drove them to a hotel where they had sex. Hotel records also showed that Wilson was the lone registered guest for room 718 on that date, police said. Court documents show there was surveillance video of this meeting.
If found guilty, Mr Wilson faces up to 20 years in prison. Last month a US judge ordered him not to post the blueprints online. The video got almost half a million views and the design was downloaded almost 100,000 times.
Years of litigation followed, leading to a settlement in July allowing Wilson to re-release the gun's downloadable blueprints.
Nineteen states and the District of Columbia sued to stop an agreement that the government reached with Defense Distributed, arguing that the blueprints could be obtained by felons or terrorists.
Later that month, Wilson said he'd started selling the plans for producing plastic firearms using 3-D printers despite an injunction blocking it.