Atomic layer deposition (ALD) is used to deposit Pt nanoparticles at low temperature (25–150 °C) to fabricate highly transparent counter electrodes (CEs) for flexible dye-sensitized solar cells (DSCs). The Pt nanoparticles (NPs) are deposited for different number of ALD cycles on indium tin oxide (ITO)/polyethylene naphthalate (PEN) substrates. Rutherford backscattering spectroscopy (RBS) and transmission electron microscopy (TEM) are used to assess the Pt NP loading, density, and size. There is a trade-off between transparency and catalytic activity of the CE, and the best cell performances of back-side-illuminated DSCs (≈3.7% efficiency) are achieved for Pt ALD at temperatures in the range of 100–150 °C, even though deposition at 25 °C is also viable. The best cell produced with ALD platinized CE (100 cycles at 100 °C) outperforms the reference cells fabricated with electrodeposited and sputtered Pt CEs, with relative improvements in efficiency of 19% and 29%, respectively. In addition, these parameters are used to fabricate a large area CE for a sub-module (active area of 17.6 cm2), resulting in an efficiency of 3.1%, which demonstrates the scalability of the process.