NAJIS started in 1981 in Detroit, Michigan, as an outgrowth of a national effort to develop an automated case management system for prosecutors. The Prosecutor Management Information System (PROMIS) was developed by INSLAW through funding provided by the Law Enforcement Assistance Administration (LEAA) in the late 1970s. One of the biggest benefits of PROMIS was the annual user group meeting. These meetings were held in different cities each year, and practitioners led discussions about successful and unsuccessful approaches to various challenges, what the future would bring, project reports, and user networking at receptions and outings. In 1981 Congress cut LEAA's funding, and agencies using the PROMIS system faced the challenge of providing on-going support for this system. This included elimination of the PROMIS user group meetings. NAJIS then began as a way to continue the PROMIS user group.

The Michigan Prosecuting Attorneys Association (PAAM) implemented PROMIS in Michigan and agreed to sponsor a meeting to set up an organization for prosecutor technical staff to discuss technology. The vision was to meet in different jurisdictions each year with various sessions where participants highlighted their technical operation, development, implementation, operational and technical challenges and solutions. Receptions and outings would be planned for user networking. For the first meeting more than 300 invitations were sent from the PROMIS user group. The two day conference was attended by 84 attendees, and included tours of the Wayne County court, prosecutor, and police operations with sessions on automation. The group met and discussed the organization and meetings resulting in the creation of the National Association for Justice Information Systems (NAJIS). Jack Stillwell, IT Director for the Arizona Prosecutor Coordinator Office, was elected Chairman of the organization. Robert Bussey, IT Director for the Colorado District Attorneys Council, was elected Treasurer. NAJIS initially focused on the use of information technology by prosecutors, and meetings were held in conjunction with the National Association for Prosecutor Coordinators (NAPC) in various locations until 1990. Each meeting drew 20 – 35 attendees.

In 1988, Kelly Bacon, Office Administrator for the Multnomah County (Portland), Oregon District Attorney's Office, attended the NAJIS meeting in Stowe, Vermont and quickly moved into a leadership role. Kelly saw the benefit of NAJIS but realized it was a fledgling organization highly dependant upon NAPC for its existence. Kelly invited the leaders of NAJIS to Portland to discuss NAJIS's organization and future. He proposed developing by-laws, incorporating as a non-profit, developing a more organized agenda, and promoting NAJIS to all members of the justice community. Through Kelly's efforts, NAJIS grew into a financially viable and formally organized association that effectively delivers on its mission to provide education and training on information technology to practitioners in the criminal justice community. Where NAJIS started as a prosecutor's IT user group, it grew into a multidisciplinary, criminal justice IT organization. In 2007, NAJIS became a federally recognized non-profit organization under section 501(c) (6), and the organization expanded its boundaries beyond prosecutorial, court, and justice related information sharing. Today, NAJIS represents government practitioners in various domains focused on the importance of data sharing best practices, thereby culminating Kelly's vision for NAJIS.

Kelly died in 1997, and the NAJIS board created the Kelly Bacon Award to recognize individuals who provide outstanding service to the justice IT community. The first award was given to Thomas Simpson (Board Member 1997 – 2001, President 2002). Other recipients include Paul Wormeli, John Goergen, Robert Greeves, and Gordon Lansford. Kelly has also been recognized through the Kelly G. Bacon Ethics in Civics Scholarship Fund and Oregon State University.