JNR Associates evolved from its founder's successful efforts to prototype the Telelogistics Document Management System, at the beginning of the rapid growth of the Internet. Mr. Jeffrey Rubin began this work in February,1996 in partnership with AIL Systems Technical Services Operations. Working out of his basement through the summer of 1996, Mr. Rubin built a prototype that demonstrated the potential of the concept and in early 1997, he and Mr. Carmine Tarantino of AIL secured the interest of Captain John O'Connell of the US Navy SPAWAR JTIDS Program Office in the project and received a contract to implement a fully functioning system.

Implementing this contract required an experienced software development team and AIL and Mr. Rubin staffed the project with a team of staff members who had been associated with his prior company. In June 1997, JNR Associates was formally incorporated in the State of Maryland.

The Company grew steadily over the years, and successfully developed the Telelogistics System into a comprehensive suite that was adopted by the USAF Computer Resources Support Improvement Program Office.  This work continued through the installation of the system at three USAF bases in 2004.

In 1999, the Company initiated a long term relationship with the Boeing/Sikorsky Comanche Helicopter Program, providing sophisticated Oracle and XML design and support services to the DIAS system that was fielded in multiple Comanche locations. This contract continued until DOD cancelled the Comanche program in 2004.

In late 2001, JNR Associates teamed with Raytheon and the US Army to develop software to concert existing legacy publications to XML.  This effort grew and eventually resulte in the IConvert software tools that provided to convert Technical Publications from legacy formats to modern XML specifications.

Raytheon Technical Services partnered with JNR Associates in 2004 and the team won two contracts from the US Army to convert paper and digital Army Depot Manuals to XML.

Using the company's experience using ATLAS and the modern C# language, JNR Associates released the ATLAS Programmer's Workbench in 2005 to increase productivity in developing Automatic Test Procedures and supplied it the US Army and US Navy..