Migratory birds globally face escalating anthropogenic threats, with crane species being particularly vulnerable. This study assessed human-perceived threats to cranes (Grus virgo & Grus grus) along Pakistan’s vital Indus Flyway using 400 stakeholder questionnaires across eight districts (2021–2024). We quantified perceived threat based on frequency (1 = Very Rare; 5 = Very Frequent) and severity (1 = Not Severe; 5 = Extremely Severe), revealing poaching (illegal killing) as the dominant threat (frequency = 4.9; severity = 4.8), followed by illegal wildlife trade (4.7; 4.5) and taming (4.6; 4.3). Spatial analysis showed strikingly higher perceived threats in southern Pakistan (Rajanpur: frequency = 4.88, severity = 4.82) versus central regions (Khushab: 3.76, 4.02; p < 0.001), with riverbanks identified as high-risk poaching zones (42 incidents). Cluster analysis also confirmed Rajanpur as a critical hotspot within three distinct threat tiers. Critically, analysis of socio-demographic drivers revealed threat type (frequency: F = 104.92, p < 0.001; severity: F = 153.64, p < 0.001) and poaching method (frequency: F = 10.14, p < 0.001; severity: F = 15.43, p < 0.001) as significant perception-shapers, while education, occupation, and crane species preference (frequency: F = 1.17, p = 0.310) exerted a non-significant influence. These results highlight that individual backgrounds minimally modulate threat perceptions. The study aligns with global evidence of uniform crane threats demanding the following urgent conservation action: region-specific enforcement (especially southern hotspots), community-led anti-poaching initiatives, and targeted awareness programs to shift high-threat communities toward crane-friendly coexistence practices.