This paper is concerned with the problem of fault-tolerant formation consensus control for linear time-varying (LTV) multi-agent systems (MASs) with stochastic communication protocol (SCP). The SCP is introduced to schedule the signal transmission, and only one neighbouring agent is allowed to transmit data at one instant. The purpose of this work is to design a fault-tolerant controller for each agent, so that, for all probabilistic scheduling behaviors, MASs can achieve the formation consensus performance. The state and fault are augmented into a new vector, meanwhile, each agent system is written as a singular one and a state observer is designed. By utilizing the estimated information of states and faults, the designed time-varying compensation term can reduce the impacts of unknown external disturbances and faults. Then, a sufficient condition is obtained to guarantee the performance constraint over the finite horizon for closed-loop systems. The parameters of observers and controllers are derived by solving coupled backward recursive Riccati difference equations. Finally, a numerical example is given to validate the effectiveness of the proposed fault-tolerant control scheme.