About 10,000 people signed a petition, and Gov. Roy Cooper even got involved.
Naimeh Salem, the father's attorney, told WSOC-TV that the visa was denied.
“They said he doesn’t have enough ties to the country to issue him a temporary visa to go to Hania's funeral,” Salem said.
Salem said they are still holding out hope that U.S. officials will have a change of heart.
Hania was taken from her home in early November.
Last week, her body was found in the water about 10 miles away.
Detectives are still searching for evidence that leads them to her killer.
The petition to the Guatemalan Embassy was circulating online to get him a non-immigrant visa.
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"They want to see that you have no intent to remain here in the U.S. if you enter on a non-immigrant visa, so they're gonna look at things people don't realize, like your income, your bank accounts, your family members, all the things that would say you are going to return to your home country,” immigration attorney Stacey Maynor said.
- Nov. 5: A man wearing all black and a yellow bandanna kidnapped Hania Aguilar from her front yard on Elizabethtown Road, forcing her into the family's SUV. Authorities issued an Amber Alert.
- Nov. 7: The FBI released surveillance video of the stolen SUV seen in Lumberton moments after the girl's kidnapping.
- Nov. 8: Authorities found the stolen SUV not far from the kidnapping scene, but there was no sign of Hania.
- Nov. 27: FBI and police find human remains off Wire Grass Road.
- Nov. 28: Preliminary test results from the medical examiner indicate body found was that of Hania.
Maynor said Hania's father would need the special visa and a green card, and the process to get one of those visas could take weeks.
“Even with enough support and contacting the right people to push it through, it is very unlikely that it's gonna happen in time for him to be here for the actual funeral,” Maynor said.
There is still a $30,000 reward for information that leads investigators to the person who killed the 13-year-old.