Laser acceleration of ions to MeV energies has been achieved on a variety of Petawatt laser systems, raising the prospect of ion beam applications using compact ultra-intense laser technology. However, translation from proof-of-concept laser experiment into real-world application requires MeV-scale ion energies and an appreciable repetition rate (>Hz). We demonstrate, for the first time, proton acceleration up to 2 MeV energies at a kHz repetition rate using a milli-joule-class short-pulse laser system. In these experiments, 5 mJ of ultrashort-pulse laser energy is delivered at an intensity near onto a thin-sheet, liquid-density target. Key to this effort is a flowing liquid ethylene glycol target formed in vacuum with thicknesses down to 400 nm and full recovery at 70 μs, suggesting its potential use at kHz rate. Novel detectors and experimental methods tailored to high-repetition-rate ion acceleration by lasers were essential to this study and are described. In addition, particle-in-cell simulations of the laser–plasma interaction show good agreement with experimental observations.