To robustly estimate the fundamental mode component of prompt neutron decay constant α in a subcritical system, dynamic mode decomposition (DMD) is applied to time-series data obtained by the pulsed-neutron source (PNS) and Rossi-α methods. For the statistical uncertainty quantification of α by DMD, randomly sampled virtual data are used for the DMD procedure. The applicability of DMD is demonstrated by analyzing the experimental results by the PNS and Rossi-α methods, which are performed at the Kyoto University Critical Assembly (KUCA). When applying the DMD to the PNS and Rossi-α experimental data, a constant signal was added to the experimental data to remove the background constant component. The application results indicate that DMD enables one to robustly estimate the fundamental mode component of α in the PNS and Rossi-α methods.