This paper presents the design and thermal characterization of a 15 × 22 mm2 LTCC module dedicated to the packaging of the elements of a miniature atomic clock. This module acts as a carrier for the components of the clock as well as temperature controller; this is particularly attractive since each component of the atomic clock requires precise and well defined working temperatures. For the thermal characterization of the designed module, various thermal simulations have been performed, by finite-element modelling using the software ANSYS; in each simulation a different experimental heating configuration was hypothesized, in order to determine the power required for achieving the desired temperature in the ideal case (module in perfect vacuum with no losses rather than conduction towards the external “cold” zone, through two small bridges) , and also for estimating the thermal losses that convection introduces into the system. The simulations were then experimentally validated by realizing and characterizing the different configurations, yielding results that were consistent with the simulations. The best experimental configuration was found, in which the heating performance was fairly close to the ideal one. The results show that LTCC is a very attractive technology for atomic clock packaging also in terms of dissipated power, provided the system is efficiently insulated.