Bonding of parts produced by fused filament fabrication (FFF) significantly depends on the temperature profile of filaments depositing one top of each other. It is necessary to evaluate the temperature profile during fabrication of structures using both theoretical and experimental approaches. This work describes the overall heat transfer (using finite volume method) that exists in such a process by taking into account the possible phenomena that are developing during the manufacturing sequence: conduction between filaments, conduction between filament and support, and convection with the environment. Although the developed model is general and applicable to both amorphous and semi-crystalline polymers and/or composites, the recordings of temperature variation at the interface of adjacent filaments of a printed vertical wall of PLA illustrated good agreement by implementing very small K-type thermocouples in parallel. It is particularly concerning the occurrence of re-heating peaks during the deposition of new filaments onto previously deposited ones. The sensitivity of the developed code to the operating conditions is shown by variation of several parameters. This makes it easy to apply it for optimization purposes. Theoretical modeling and experimental data presented in this study help better understanding of heat transfer existing in polymer/composite additive manufacturing, and can be valuable to predict more accurately the bond quality and apply the obtained findings for further steps.