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Wheat leaf rust fungus is an obligate parasitic fungus that can absorb nutrients from its host plant through haustoria and secrete effector proteins into host cells. The effector proteins are crucial factors for pathogenesis as well as targets for host disease resistance protein recognition. Exploring the role of effector proteins in the pathogenic process of <i>Puccinia triticina Eriks.</i> (<i>Pt</i>) is of great significance for unraveling its pathogenic mechanisms. We previously found that a cysteine-rich effector protein, Pt1641, is highly expressed during the interaction between wheat and <i>Pt</i>, but its specific role in pathogenesis remains unclear. Therefore, this study employed techniques such as heterologous expression, qRT-PCR analysis, and host-induced gene silencing (HIGS) to investigate the role of Pt1641 in the pathogenic process of <i>Pt</i>. The results indicate that Pt1641 is an effector protein with a secretory function and can inhibit BAX-induced programmed cell death in <i>Nicotiana benthamiana</i>. qRT-PCR analyses showed that expression levels of <i>Pt1641</i> were different during the interaction between the high-virulence strain THTT and low-virulence strains FGD and Thatcher, respectively. The highest expression level in the low-virulence strain FGD was four times that of the high-virulence strain THTT. The overexpression of <i>Pt1641</i> in wheat near-isogenic line TcLr1 induced callose deposition and H₂O₂ production on TcLr1. After silencing <i>Pt1641</i> in the <i>Pt</i> low-virulence strain FGD on wheat near-isogenic line TcLr1, the pathogenic phenotype of <i>Pt</i> physiological race FGD on TcLr1 changed from “;” to “3”, indicating that Pt1641 plays a non-toxic function in the pathogenicity of FGD to TcLr1. This study helps to reveal the pathogenic mechanism of wheat leaf rust and provides important guidance for the mining and application of <i>Pt</i> avirulent genes.