Peralta made over 20 international appearances and moved to Olimpia earlier this year after spending a year and a half with Scottish club Rangers.
"We deeply regret the death of our player Arnold Peralta. The Olympic family is mourning," Olimpia tweeted.
The Honduran football federation also sent their commiserations to the family and friends of Peralta, who was 26.
Peralta, who played as a defensive midfielder, represented Honduras several occasions, including multiple World Cup qualifiers.