H7N9 is an avian strain of the species Influenza virus that circulates among avian populations. Occasionally, some variants of this strain were known to infect humans. On March 30, 2013, a novel avian influenza A H7N9 virus that infects human beings was identified in China. In February 2014, the first case of H7N9 infection outside China was reported in Malaysia involving a Chinese tourist. This study was aimed to characterize the first case of H7N9 in Malaysia by means of molecular identification, sequencing of hemagglutinin (HA) and neuraminidase (NA) genes, and phylogenetic analysis. The patient was confirmed positive for H7N9 virus by real-time RT-PCR (rRT-PCR). Subsequently, the samples were sequenced and mutation analysis identified R65K, E122K, L186I and N285D mutations in HA gene and M26I, R78K and V345I mutations in NA gene. We reported the emergence of a new mutation L186I, not found in the current database of any H7N9 sequences. Mutations associated with drug resistance were not found in this patient. Phylogenetic analysis revealed that the HA gene is closely related to the group of strains from Guangzhou, whereas NA gene is closely related to the group of strains from Guangdong. The present study provides crucial information on the first case of H7N9 outside China and the diversity of this strain from other reported H7N9 strains by molecular analysis.