Coupled-resonator microstrip filters are among the most versatile filter topologies. A known design approach uses full-wave electromagnetic simulations to determine the coupling coefficient between resonators as a function of their relative position. This could be done using time-domain simulations using a fast Fourier transform (FFT) to extract the couplings from the S parameters obtained from time-domain signals. However, this approach has a poor performance in terms of resolution and specially for weak couplings, leading to unreasonably long simulation times. To overcome this, we introduce a technique to obtain the couplings directly from time signals, without moving to the frequency domain. This procedure works for strong and weak couplings, with much shorter simulation times and a reduced simulation domain over the FFT approach. This technique is used to design coupled resonator filter efficiently from time domain simulations. We implement this procedure using the finite-difference time-domain framework using an open source solver and discuss our implementation. We show that its results are very similar to previously published ones obtained from frequency domain simulations, even in the case of very weak couplings. Finally, we design and measure a filter to show the good performance of the proposed approach.