In this paper, we study the joint design of transmitted sequence and receiving filter to improve the performance of radar in the presence of Doppler shifts. The mean-square error (MSE) of the estimates of the scattering coefficients of the pointlike targets is considered to be the figure of merit. The design problem is cast as a joint optimization problem to minimize the MSE in the presence of target and clutter Doppler shifts. To tackle the design problem, we devise a new data model with respect to the Doppler shifts and propose a cyclic iterative approach to obtain optimized pairs for receiving filters and transmitted sequences. The proposed approach is based on fractional programming and iterations of the power method, and this approach is computationally efficient. Moreover, this approach can handle unimodularity constraints, quantization constraints, and peak-to-average power ratio constraints on the transmitted sequence. Simulation examples show the effectiveness of the proposed approach.