He was getting on the Sunmi on the River Thames at Gravesend Reach in Kent at about 18:10 BST on Wednesday when it happened, the PLA said.
Emergency services were called but were unable to save him, the authority said.
PLA chief executive Robin Mortimer said: "Our deepest condolences are with our colleague's family and friends at this very difficult time."
He added: ""We have been in touch with the family and are offering whatever support we can."
No details of the nature of the accident have been revealed by the PLA.
The authority and the Marine Accident Investigation Branch have started an investigation into the accident and will be attending the PLA's Gravesend base on Thursday.
A Port of London Authority (PLA) river pilot has been killed in an accident while boarding a ship.