Tuberculosis lymphadenitis is the frequent form of extra pulmonary tuberculosis (EPTB). Fine needle technique is easy to be carried out by trained healthcare workers in resources limited setting like Nigeria. This case report was aimed to highlight use and challenges of fine-needle aspirate biopsy (FNAB) for GeneXpert MTB/RIF assay in the diagnosis of EPTB. Fine needle aspirate was taken from left lymph node and processed for cytological staining with Diff Quik and Ziehl Neelsen stains (ZN) as well as GeneXpert molecular assay. The Diff Quick and ZN showed necrotic debris with epithelioid histiocytes and occasional giant cells while ZN was negative. GeneXpert result reveals Mycobacterium tuberculosis Complex and Rifampicin resistance not detected. These findings provided quick and effective means of diagnosis of EPTB especially from FNAB which has not been commonly undertaken in resource limited Nigeria. J Microbiol Infect Dis 2020; 10(1):59-61.