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This study proposes a novel flexible hybrid state estimation (SE) algorithm when a realistic communication system with its irregularities is taken into account. This system is modelled by the Network Simulator 2 software tool, which is also used to calculate communication delays and packet drop probabilities. Within this setup, the system observability can be predicted, and the proposed SE can decide between using the static SE (SSE) or the discrete Kalman filter plus SSE‐based measurements and time alignment (Forecasting‐aided SE). Flexible hybrid SE (FHSE) incorporates both phasor measurement units and supervisory control and data acquisition‐based measurements, with different time stamps. The proposed FHSE with detailed modelling of the communication system is motivated by: (i) well‐known issues in SSE (time alignment of the measurements, frequent un‐observability for fixed SE time stamps etc.); and (ii) the need to model a realistic communication system (calculated communication delays and packet drop probabilities are a part of the proposed FHSE). Application of the proposed algorithm is illustrated for examples with time‐varying bus load/generation on two IEEE test cases: 14‐bus and 300‐bus.