Silicon-based single-photon avalanche diodes (SPADs) implemented in front-side illuminated arrays and imagers have often suffered from fill factor limitations. The corresponding reduced sensitivity can be sometimes traded off with longer acquisition times thanks to SPAD’s noiseless read-out. The use of SPADs can however be critically affected in many applications, especially when photon-starved, or when several photons need to be detected in coincidence. The fill factor loss can be recovered by employing microlens arrays, which are difficult to build with relatively large pitch (> 10 μm) and low native SPAD fill factor (as low as 10%). To address these challenges, we have developed several generations of refractive microlenses by photoresist reflow used to fabricate molds. These structures were used to imprint UV-curable hybrid polymer microlenses on SPAD arrays. Replications were successfully carried out on large SPAD arrays with very thin residual layers (~10 μm), as required for higher numerical aperture (NA > 0.25). Replications were also carried out for the first time in a multi-chip operation regime at the wafer reticle level. By optimizing the lens sag and residual layer thickness, concentration factors (CFs) within 15-20% of the theoretical maxima were obtained for the smaller arrays (32×32 and 512×1). The spectral response was flat above 400 nm. CF values up to 4.2 with good uniformity were measured on large 512×512 arrays with 16 μm pixel pitch and a native fill factor of 10.5%. This result was confirmed by simulations when using the actual measured lens shape. We thus demonstrated good spectral and spatial uniformity and high CF, while moving to higher NAs and larger sensor sizes with respect to previous work.