Apptricity, based in Texas, has provided logistics programs to the army since 2004.
The company said it had discovered last year the software had been installed on many more machines than had been licensed.
The Department of Justice (DoJ) has not commented on the settlement.
The Dallas Morning News reported a DoJ spokeswoman had confirmed the agreement, but would not give more details.
Apptricity’s software allows the military to track the movements of soldiers as well as key supplies.
It has also been used during relief efforts, most notably in Haiti following the 2010 earthquake.
According to court documents filed in 2012, the deal with the military meant up to 500 named users could access the software.
Apptricity later estimated that 9,000 users were accessing the program, in addition to the 500 that had been paid for.
The unauthorized copying only came to light after a US Army official mentioned “thousands” of devices running the software during a presentation on technology.
Apptricity called for $224 million to be paid to cover costs.
The settlement of $50 million falls some way short – but in a statement the company said Apptricity would spend the sum on expanding the company.
“Apptricity is now incredibly energized to use the settlement resolution as a catalyst for aggressive investment in our team, our solutions and our untapped market opportunities,” said Randy Lieberman, Apptricity’s chief financial officer.
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