The thermal and mechanical perfection of the processes in the gas exchange system during the filling and emptying of the cylinder makes it possible to increase the productivity and efficiency of reciprocating machines for various purposes. The study was designed to obtain experimental data on the local heat transfer of pulsating flows in the intake and outlet pipelines of a piston engine model, their analysis, and mathematical description. The scientific novelty of the study is as follows: (1) the patterns of change in the local heat transfer coefficients of pulsating gas flows in the inlet and outlet pipelines for the piston engine model were obtained for the first time; (2) a mathematical description of the experimental data on local and average heat transfer in the inlet and outlet pipelines is proposed. The physical features of the change in the rate of heat transfer in the intake and exhaust systems for a full engine cycle are discussed. A spectral analysis of the harmonic functions of the change in the local heat-transfer coefficient in gas exchange systems is performed. A set of mathematical dependencies of changes in the local and average heat-transfer coefficients of flows in the inlet and outlet pipelines on operation factors are presented. These data can be used to assess the quality of filling and cleaning the cylinder, determining thermal stresses in the details of gas exchange systems, developing devices for using exhaust gas energy, creating engine control systems, and so on. Moreover, the results obtained can be used to adjust (and test) mathematical models, as well as refine engineering methods for calculating gas exchange processes in reciprocating machines for various purposes.