End-to-end delay measurement has been an essential element in the deployment of real-time services in networked systems. Traditional methods of delay measurement based on time domain analysis, however, are not efficient as the network scale and the complexity increase. We propose a novel theoretical framework to analyze the end-to-end delay distributions of networked systems from the frequency domain. We use a signal flow graph to model the delay distribution of a networked system and prove that the end-to-end delay distribution is indeed the inverse Laplace transform of the transfer function of the signal flow graph. Two efficient methods, Cramer's rule-based method and the Mason gain rule-based method, are adopted to obtain the transfer function. By analyzing the time responses of the transfer function, we obtain the end-to-end delay distribution. Based on our framework, we propose an efficient method using the dominant poles of the transfer function to work out the bottleneck links of the network. Moreover, we use the framework to study the network protocol performance. Theoretical analysis and extensive evaluations show the effectiveness of the proposed approach.