San Juan County Commissioners voted Tuesday to approve the charge for the service, which has been offered free.
County Operations Officer Mike Stark said the county decided to start charging for the service to cover some of the taxpayer expense for fingerprinting. He said the $5 fee per set of fingerprints doesn't cover the county's entire fingerprinting cost.
"It's not meant to be a source of revenue," he said.
San Juan County Detention Center Administrator Tom Havel said a $5 fee per set of fingerprints is similar to what other governments charge for the service.
Since August 2011, the county has given 2,743 people 6,147 sets of fingerprints, according to county documents.
At $5 per set, the county would have collected $30,735 under the rate approved Tuesday.
Tuesday's vote does not mean that inmates or registered sex offenders will have to pay to be fingerprinted, Stark said.
The county offers fingerprinting on weekdays at the San Juan County Sheriff's Office and on weekends at the San Juan County Detention Center.
Detention Center Officer Charles Greenfield said the common reasons people request fingerprints are when they are apply for jobs within local school district and certain government jobs.
People also need to be fingerprinted when they apply for a concealed-carry permit.
Fingerprinting takes about 15 minutes per person to complete and most people who are fingerprinted request two or three copies, said Louise Vanhuss, the sex offender program technician for the sheriff's office.
Vanhuss said the sheriff's office will post a notice of the new administrative fee on its door for about two weeks before it implements the fee.