Two-dimensional (2D) transition metal dichalcogenide (TMD) materials have exceptional optoelectronic and structural properties, which allow them to be utilized in several significant applications in energy, catalyst, and high-performance optoelectronic devices. Among other properties, the nonlinear optical properties are gaining much attention in the research field. In this work, a unique pentagonal TMD material, palladium disulfide (PdS₂), is employed as a saturable absorber (SA) in an ytterbium-doped fiber (YDF) laser cavity and mode-locked laser pulse is generated. At first, liquid phase exfoliation is performed to prepare PdS₂ nanoflakes. Afterward, the PdS₂-nanoflakes solution was incorporated in the side-polished fiber (SPF) to form SPF-based PdS₂-SA. By utilizing this SA, a highly stable mode-locked laser pulse is realized at pump power of 160 mW, which has a center wavelength of 1033 nm and a 3-dB spectral bandwidth of 3.7 nm. Moreover, the pulse duration, maximum power output and corresponding single-pulse energy were determined as 375 ps, 15.7 mW and 0.64 nJ, respectively. During the experiment, the mode-locked pulse remained stable till the pump power reached a value of 400 mW and, for the regulation of power, the slope efficiency is calculated at about 4.99%. These results indicate that PdS₂ material is a promising nonlinear optical material for ultrafast optical applications in the near-infrared (NIR) region.