Abstract Juno was inserted into a polar orbit about Jupiter on July 4th 2016. Juno's magnetic field investigation acquires vector measurements of the Jovian magnetic field using a pair of a tri-axial Fluxgate Magnetometers (FGM) co-located with four attitude-sensing star cameras on an optical bench. The optical bench is placed on a boom at the outer extremity of one of Juno's three solar arrays. The Magnetic Field investigation (MAG) uses measurements of the optical bench inertial attitude provided by the micro Advanced Stellar Compass (μASC) to render accurate vector measurements of the planetary magnetic field. During periJoves, orientation of the MAG Optical Benches (MOB) is determined using the spacecraft (SC) attitude combined with transformations between SC and MOB coordinate frames. Substantial pre-launch effort was expended to maximize the thermo-mechanical stability of the Juno solar arrays and MAG boom. Nevertheless, the Juno flight experience demonstrates that the transformation between SC and MAG reference frames varies significantly in response to spacecraft thermal excursions associated with large attitude maneuvers and proximate encounters with Jupiter. This response is monitored by comparing attitudes provided by the MAG investigation's four Camera Head Units (CHUs) with those provided by the Stellar Reference Unit (SRU). These systematic variations in relative orientation are thought to be caused by the thermo-elastic flexure of the Juno solar array in response to temperature excursions associated with maneuvers and heating during close passages of Jupiter. In this paper, we investigate these thermal effects and propose a model for compensation of the MAG boom flexure.