Zirconium (Zr) thin films deposited on Si (100) by pulsed laser deposition (PLD) at different pulse repetition rates are investigated. The deposited Zr films exhibit a polycrystalline structure, and the X-ray diffraction (XRD) patterns of the films show the α Zr phase. Due to the morphology variation of the target and the laser-plasma interaction, the deposition rate significantly decreases from 0.0431 Å/pulse at 2 Hz to 0.0189 Å/pulse at 20 Hz. The presence of droplets on the surface of the deposited film, which is one of the main disadvantages of the PLD, is observed at various pulse repetition rates. Statistical results show that the dimension and the density of the droplets increase with an increasing pulse repetition rate. We find that the source of droplets is the liquid layer formed under the target surface. The dense nanoparticles covered on the film surface are observed through atomic force microscopy (AFM). The root mean square (RMS) roughness caused by valleys and islands on the film surface initially increases and then decreases with the increasing pulse repetition rate. The results of our investigation will be useful to optimize the synthesis conditions of the Zr films.