The current study was designed to investigate the molecular characterization and pathological potential of field isolated H9N2 low pathogenic avian influenza virus (LPAIV). Trachea, lungs, kidney, and spleen tissue samples of 413 chickens with respiratory signs were collected from one hundred poultry flocks, processed for RT-PCR, phylogenetic analysis, and histopathological examinations. A PCR product of 918 bp corresponding to a fragment of the HA gene was detected in 14 samples. After nucleotide sequencing and alignment, the positive samples were grouped into two isolates. Field isolates of the current study have 95.02-98.85% nucleotide and 90.04-98.21% amino acid homology to previously reported H9N2 strains from Pakistan. Microscopic examination revealed degenerative changes, necrosis, congestion, hemorrhages, and mononuclear cell infiltration in the trachea, lungs, kidney, and spleen. Based on the molecular analysis, the results depicted that studied isolates shared 95.02-98.85% nucleotide identity, and 90.04-98.21% amino acid similarity with other Pakistan originated H9N2 LPAIV and referenced A/Quail/Hong Kong/G1/97 isolates, hence, clustered in G1-lineage. Moreover, H9N2 LPAIV also induced gross and microscopic alternations in the studied organs. Further investigations on potential transmission risks, pathotyping, and causes of vaccine failures are required.