The development of highly efficient near infrared (NIR) luminescence materials is crucial for advancing the next generation compact light sources. However, the realization of target material with emission in the NIR-II spectral region (1000–1700 nm) remains a major challenge. Herein, a NIR-II emission phosphor Ba3BPO7:Mn5+ peaking at 1176 nm with a full width of half maximum of 22 nm is demonstrated via a selective site occupancy engineering strategy. Upon 660 nm red-light excitation, high internal quantum efficiency of 50.6% and external quantum efficiency of 30.5% are obtained in this phosphor. Density functional theory calculations and structural analyses provide an understanding of stabilizing pentavalent manganese in Ba3BPO7:Mn5+. The highly efficient NIR-II emission is mainly ascribed to the relatively high distorted tetrahedral crystal field environment of Mn5+ in this system and the stable valence state. Combining this phosphor with 660 nm red-light chip, we fabricate a light emitting diode with NIR-II output power of 19.2 mW@300 mA, which shows promising applications in anti-counterfeiting, special information identification, etc. This work provides some important insights into the design of highly efficient Mn5+ based NIR-II emission and the emerging applications.