Everton board members chief executive Denise Barrett-Baxendale, chief finance and strategy officer Grant Ingles and non-executive director Graeme Sharp are leaving their roles.
Chairman Bill Kenwright's position is also being assessed over the next 48 hours.
The departing directors said in a joint statement: "We have all been fully committed during our time here and are disappointed to have made the decision to leave Everton.
"We have worked tirelessly alongside our chairman in what has been a challenging period to deliver some of the most significant projects in Everton's history - projects that will safeguard and sustain the commercial future of the club for generations to come.
"We are proud of the commercial growth projects progressed during our time on the board, including the construction of the club's new waterfront stadium. This construction project - the largest currently on site in the UK - is progressing at pace.
"The club's partnership portfolio has also been increased and diversified, reflected in record commercial partnerships and the expansion of our work internationally."
Kenwright added: "This has been a great board who have all worked tirelessly for the club, no matter what the circumstances.
"My relationship with Denise has been known as one of the closest in football. I thank her for her many achievements, particularly her magnificent work in respect of our new stadium."