In this paper, topology identification of dynamic systems in the continuous time (CT) framework is considered. The main objective is to identify the direction of information flow and to estimate the transfer function of each node simultaneously. The output of each node is affected by the outputs of the other nodes along with transportation delay and noise. In contrast to the existing works which are in discrete setting, the current paper uses continuous orthonormal basis to represent the transfer functions. As the network is sparsely connected, the topology identification problem is defined as an estimation of a block-sparse signal from the measurements and a standard l0 minimization algorithm known as the block orthogonal matching pursuit (BOMP) is used to identify the topology. The accuracy of the proposed method is demonstrated using data obtained from a system of interconnected tanks. A comparison with discrete time topology identification methods shows that the CT method is more robust and provides the exact topology with higher probability. © 2018 IEEE.