This paper presents a computer simulation model (in the MATLAB/Simulink environment) of a photovoltaic system disturbed by a 1.2/50 µs voltage surge pulse, while operating as part of the fixed system of an intelligent building. The tested part of the system consisted of a single PV module and a single-phase DC/AC voltage source converter provided with a maximum power point tracking system. The simulation of the test performed in accordance with the IEC 61000-4-5 standard required the development of a model of a surge waveform generator and a model of a coupling/decoupling network. The 1.2/50 μs voltage surge pulse was introduced into the system from the power grid side. During the test significant changes in the value of the AC voltage and current were found in the DC/AC converter system. The results of the computer simulation tests were verified with measurements performed in an accredited electromagnetic compatibility laboratory using the instructions specified in IEC 61000-4-5. The MATLAB/Simulink environment was proved as a useful tool of the assessment of effects of conducted electromagnetic disturbances on electronic/electric devices.