You’ll need to travel to Maya in the north of Cebu and take a boat across to Malapascua. You can take a large air-conditioned bus which stops on route and takes 5 hours. Smaller, non air-conditioned buses take around 4 hours non-stop. Buses depart frequently throughout the day from Cebu Airport and the city. Taxi’s are more expensive but take only 2.5 hours. Boats leave when they are full but if you want to leave sooner, expect to pay more or opt for a private boat. The crossing from Maya to Malapascua takes 30 minutes.
Note - Travel to any destination may be adversely affected by conditions including (but not limited) to security, entry and exit requirements, health conditions, local laws and culture, natural disasters and climate. Regardless of your destination, check your local travel advisory board or department for travel advice about that location when planning your trip and again shortly before you leave.