The auxin efflux carrier PIN-FORMED (PIN) family is pivotal for generating asymmetric auxin distribution that orchestrates plant root development. While the monocot-specific OsPIN9 has been implicated in tillering and stress responses, its precise role in early root development remains unclear. Here, we demonstrate that OsPIN9 functions at the plasma membrane to maintain optimal auxin levels for root system architecture in rice. We confirmed its plasma membrane localization using a GFP fusion within the central hydrophilic loop, minimizing functional interference. Intriguingly, both knockout and overexpression of OsPIN9 resulted in similar defective phenotypes, including shorter roots and reduced crown and lateral roots. These defects were partially rescued by exogenous auxin, and overexpression lines exhibited resistance to the auxin transport inhibitor N-1-naphthylphthalamic acid (NPA). Furthermore, independent OsPIN9-GFP lines reproduced the overexpression phenotypes. Additionally, transcriptomic profiling revealed that loss of OsPIN9 function alters the expression of key genes involved in auxin transport and biosynthesis, providing a molecular basis for the disturbed auxin homeostasis underlying the root defects. Our findings define OsPIN9-mediated polar auxin transport as being essential for auxin homeostasis, thereby orchestrating the establishment of the root system in early seedlings.