Two-dimensional (2D) niobium carbide, Nb4C3Tx (Tx: O, OH, and F), a representative member of the 43 MXene structural motif, has shown promising electrochemical performance in acidic electrolytes. The capacitive performance of Nb4C3Tx in neutral aqueous electrolytes has been reported as moderate, but little effort has been made to improve it. In this paper, we report a method to introduce nanopores (pinholes) in Nb4C3Tx MXene flakes by adjusting the etching time. The pinholes generated during the etching process improve ion diffusion pathways, which are otherwise hindered by the restacking of the 2D flakes. The “holey Nb4C3Tx” shows a 50 % improved rate capability at charge/discharge time scales of 1–2 s in 1 M Li2SO4, Na2SO4, and (NH4)2SO4 electrolytes. Our strategy of controlling the permeability of Nb4C3Tx sheets can potentially be applied to other MXenes, providing guidance for improving the capacitance and rate capability of 2D materials. © 2022 The Author(s)