The Aerospace Corporation (Aerospace) and Lockheed Martin Space Systems (LMSS) participated with Jet Propulsion Laboratory (JPL) in the implementation of a magnetic cleanliness program of the NASA/JPL JUNO mission. The magnetic cleanliness program was applied from early flight system development up through system level environmental testing. The JUNO magnetic cleanliness program required setting-up a specialized magnetic test facility at Lockheed Martin Space Systems for testing the flight system and a testing program with facility for testing system parts and subsystems at JPL. The magnetic modeling, simulation and analysis capability was set up and performed by Aerospace to provide qualitative and quantitative magnetic assessments of the magnetic parts, components, and subsystems prior to or in lieu of magnetic tests. Because of the sensitive nature of the fields and particles scientific measurements being conducted by the JUNO space mission to Jupiter, the imposition of stringent magnetic control specifications required a magnetic control program to ensure that the spacecraft's science magnetometers and plasma wave search coil were not magnetically contaminated by flight system magnetic interferences. With Aerospace's magnetic modeling, simulation and analysis and JPL's system modeling and testing approach, and LMSS's test support, the project achieved a cost effective approach to achieving a magnetically clean spacecraft. This paper presents lessons learned from the JUNO magnetic testing approach and Aerospace's modeling, simulation and analysis activities used to solve problems such as remnant magnetization, performance of hard and soft magnetic materials within the targeted space system in applied external magnetic fields.