The Warn-on-Forecast (WoF) program, driven by advanced data assimilation and ensemble design of numerical weather prediction (NWP) systems, seeks to advance 0–3-h NWP to aid National Weather Service warnings for thunderstorm-induced hazards. An early prototype of the WoF prediction system is the National Severe Storms Laboratory (NSSL) Experimental WoF System for ensembles (NEWSe), which comprises 36 ensemble members with varied initial conditions and parameterization suites. In the present study, real-time 3-h quantitative precipitation forecasts (QPFs) during spring 2016 from NEWSe members are compared against those from two real-time deterministic systems: the operational High Resolution Rapid Refresh (HRRR, version 1) and an upgraded, experimental configuration of the HRRR. All three model systems were run at 3-km horizontal grid spacing and differ in initialization, particularly in the radar data assimilation methods. It is the impact of this difference that is evaluated herein using both traditional and scale-aware verification schemes. NEWSe, evaluated deterministically for each member, shows marked improvement over the two HRRR versions for 0–3-h QPFs, especially at higher thresholds and smaller spatial scales. This improvement diminishes with forecast lead time. The experimental HRRR model, which became operational as HRRR version 2 in August 2016, also provides added skill over HRRR version 1.