The thermal regulation problem for a lithium ion (Li-ion) battery with boundary control actuation is considered. The model of the transient temperature dynamics of the battery is given by a nonhomogeneous parabolic partial differential equation (PDE) on a two-dimensional spatial domain which accounts for the time-varying heat generation during the battery discharge cycle. The spatial domain is given as a disk with radial and angular coordinates which captures the nonradially symmetric heat-transfer phenomena due to the application of the control input along a portion of the spatial domain boundary. The Li-ion battery model is formulated within an appropriately defined infinite-dimensional function space setting which is suitable for spectral controller synthesis. The key challenges in the output feedback model-based controller design addressed in this work are: the dependence of the state on time-varying system parameters, the restriction of the input along a portion of the battery domain boundary, the observer-based optimal boundary control design where the separation principle is utilized to demonstrate the stability of the closed loop system, and the realization of the outback feedback control problem based on state measurement and interpolation of the temperature field. Numerical results for simulation case studies are presented. (c) 2013 American Institute of Chemical Engineers AIChE J, 59: 3782-3796, 2013