The young duo, recently inducted into the border guarding force, shot each other using their service weapons and were a 'buddy pair' tasked to secure the frontier in Anupgarh's Shivni area in Sriganganagar sector of the border.
The bodies of the jawans, identified as Jitender and Badal, were recovered by BSF officials who rushed to the spot after they heard gunshots at 3 am.
The officials found the troops lying in a pool of blood in a trench near the border post.
Jitender, according to sources, pumped 12 bullets from his Light Machine Gun (LMG) into Badal, who instead got two fatal bullet shots from the INSAS rifle of his fellow trooper.
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Senior officials have recovered empty cartridges from the spot and have ruled out any foul play from across the border or by any third party.
"The exact reason as to why the young boys did this is yet to be known. A Court of Inquiry is underway," a senior official said.
Jitender belonged to Meerut while Badal hailed from Bulandshahar, they said, adding their bodies are being sent to their respective home towns.
This is the third reported case of fratricide in the force this year.
In an similar incident in January, two BSF jawans killed each other in the Punjab sector.