Rationale: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been recognized as highly pathogenic. The current pandemic of SARS-CoV-2 has been spread globally and infected more than 200 countries. Patient concerns: We report the first confirmed fatal case of COVID-19 in Pakistan. A 50-year-old man returned from Saudi Arabia on March 09, 2020 and presented with cough, fever, malaise, poor appetite and difficulty in breathing to the Pulmonologist at District Headquarter Hospital Mardan. Diagnosis: The patient was initially diagnosed as COVID-19 suspected case. A oropharyngeal swab sample was positive by realtime RT-PCR tests. Lessons: This report highlights the importance of close coordination between clinicians and public health authorities as well as the importance of early laboratory-based confirmation of COVID-19 cases.