On 02 September 2002 the JALLC opened its doors for business for the first time. The precursor body to the JALLC was the Permanent Maritime Analysis Team (PAT) based at Northwood, UK, which conducted operational analysis of NATO maritime exercises using a staff predominantly composed of naval officers. The PAT, suitably augmented, formed the core of the team tasked with analysis of the NATO Implementation Force (IFOR) and Stabilization Force (SFOR) operations in the Former Yugoslavia. The final report by the IFOR Joint Analysis Team recognized the lack of a standing NATO joint analysis capability, which led to the formation of a NATO Working Group tasked to develop the concept for a JALLC.

The operational requirement for the JALLC was approved by the NATO Military Committee (MC) in June 1997 and the detailed the JALLC implementation concept, which also recommended that the JALLC be located in Portugal, was approved by the MC on 07 December 2001. The JALLC was activated on 02 September 2002, was formally opened on 06 December 2002 and declared full operational capability on 28 March 2006.

The JALLC's present staff celebrated the JALLC's 16th birthday with an informal barbeque in the JALLC's courtyard. The Commander toasted the JALLC and wished everyone, including the distinguished guests from the Portuguese Air Force base, which hosts the JALLC, happiness and good health.