Introduction The COVID-19 pandemic has profoundly impacted medical practices, including nuclear medicine. To minimize aerosol transmission risks, lung perfusion scintigraphy was preferred over traditional ventilation-perfusion (V/Q) scintigraphy during the pandemic. This study compares lung perfusion scans performed during COVID-19 with V/Q scans from the pre-COVID era. After reviewing this study, the reader will learn about V/Q scintigraphy and lung perfusion. Methods This retrospective observational study, conducted from December 2018 to July 2021, involved 868 patients - 511 in the pre-COVID era and 357 in the post-COVID era - at a single tertiary care center. The pretest probability of pulmonary embolism (PE) was determined using Wells' criteria, and data including demographics, clinical findings, and diagnostic test results (V/Q or lung perfusionscintigraphy) were collected. Results A 30% decline in lung scans was observed during the pandemic. In the pre-COVID era, 68.3% of scans had low, 27.8% had intermediate, and 3.9% had high probability for PE. During the pandemic, perfusion-only scans showed 57.3% low, 32.9% indeterminate, and 9.8% high probability for PE. Among COVID-19-positive patients, 48.9% had intermediate, and 11.1% had high probability scans. The rise in indeterminate and high-probability scans during the pandemic is attributed to COVID-19-related lung changes and hypercoagulability. Conclusion The perfusion component of lung scans is typically sufficient for evaluating acute PE. Omitting the ventilation part of the V/Q scan had minimal impact, with only a 5.1% increase in indeterminate/non-diagnostic scans using perfusion-only modified Prospective Investigation of Pulmonary Embolism Diagnosis II (PIOPED II) criteria during the post-COVID-19 era, likely due to underlying lung parenchymal involvement in COVID-19 patients. Additionally, there was a 5.9% rise in high-probability scans, attributed to the hypercoagulability and vascular complications associated with COVID-19.