Polyisobutylene (PIB) is commonly used as a primary sealant in multi-layer insulating glazing elements, where temperatures often exceed 100 °C. At such conditions, PIB undergoes structural changes, causing different relaxation dynamics and leading to decreased lifetime of the material. Understanding thermal behavior is therefore imperative for achieving effective insulation of these materials for long-term use in insulating application. The present study was focused on the temperature dependence of viscoelastic behavior of two commercially available polyisobutylene (PIB) materials, which are commonly used as primary sealants for energy-efficient multi-layer glazing units. The long-term viscoelastic behavior of the materials before and after thermal treatment at high temperatures was studied by using time–temperature superposition (tTS). Van-Gurp–Palmen plots were obtained directly from experimental data and enabled the study of thermally induced changes, while the relaxation time spectra were calculated from master curves and enabled the calculation of molecular weight distribution. The results showed that, after thermal treatment, the structure of PIB materials changes from linear to branched, while the molecular weight distributions transition from monomodal to bimodal. The untreated samples exhibited viscous-like behavior, while the thermally stabilized samples exhibited solid-like behavior, extending the material response for ~6 decades towards a longer timescale. Moreover, the presented results can be directly used to simulate the mechanical responses of the sealants using currently available FEM software packages to predict their functional and structural lifetime.