"I was first elected to this job seven years ago because our national federations wanted transparency, good governance and change and I promised a transformational presidency," Princess Haya said.
She used her first term to modernize rules governing use of medications and banned drugs after several medal-winning horses were disqualified for positive doping tests at the 2008 Beijing Olympics.
However, the FEI's recent focus on developing endurance racing and long-term plan to win Olympic status for the discipline had raised concerns.
Princess Haya's husband, Sheik Mohammed bin Rashid Al Maktoum, the ruler of Dubai, is an influential competitor and supporter of endurance racing.
Princess Haya would also lose her International Olympic Committee membership on leaving the FEI. She was elected in 2007 through her position as a governing body president.