In this article, we reveal the effect of ultralow concentration of Y dopant on the formation, structure peculiarities and optical properties of yttrium-doped ZnO (YZO) films. The YZO films were deposited on glass substrates at 250 °C and at room temperature (HT and RT, correspondingly) with the magnetron co-sputtering method in a direct current (DC) regime. The Y content in the ZnO matrix was varied by DC power applied to the Y target, and did not exceed 0.14 and 0.11 at.% for RT and HT regimes, correspondingly. For the first time it was revealed that the presence of ultralow Y dopant in the co-sputtering process at RT abruptly increases the growth rate of the YZO films by 20%, enlarges the size of crystallites and degree of texture, and cardinally changes the morphology. For the HT regime, the smooth increasing of the deposition rate and the morphological changing of the YZO films with an increase in the Y content were registered. The deposited YZO films demonstrated a high level of optical transparency in the visible and IR region. Ultralow Y doping of ZnO led to decreasing of the bandgap width. The ZnO and YZO films possessed the resistivity typical for insulators even at the highest Y content at both RT and HT deposition regimes.