Juno was inserted into a highly elliptic, polar, orbit about Jupiter on July 4th 2016. Juno’s magnetic field investigation acquires vector measurements of the Jovian magnetic field using a flux gate magnetometer co-located with 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, MAG orientation is determined using the spacecraft (SC) attitude combined with transformations between SC and MAG. Substantial pre-launch efforts were expended to maximize the thermal and mechanical stability of the Juno solar arrays and MAG boom. Nevertheless, flight experience demonstrated that the transformation between SC and MAG reference frames varied 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 CHU’s and the spacecraft attitude. These attitude disturbances are 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 effect.