The effects of both external squeezing and internal pressure pulsations are studied on flow and heat transfer inside non-isothermal and incompressible thin films supported by soft seals. The laminar governing equations are non-dimensionalized and reduced to simpler forms. The upper plate displacement is related to the internal pressure through the elastic behavior of the supporting seals. The following parameters: squeezing number, squeezing frequency, frequency of pulsations, Fixation number (for the seal) and the thermal squeezing parameter are found to be the main controlling parameters. Accordingly, their influences on flow and heat transfer inside disturbed thin films are determined and discussed. It is found that an increase in the Fixation number results in more cooling and a decrease in the average temperature values. Also, it is found that an increase in the squeezing number decreases the turbulence level at the upper plate. Furthermore, fluctuations in the heat transfer and the fluid temperatures can be maximized at relatively lower frequency of internal pressure pulsations.