The 800-kilowatt turbine on outlying Lamma Island was commissioned in 2006 to explore the potential of wind energy for the southern Chinese city.
HK Electric said the equipment had reached the end of its 20-year service life and that the facility had "successfully completed its role".
"As most of its specialised components and spare parts are no longer produced, and no compatible commercial wind turbine models are available for direct replacement at the site, HK Electric has determined that decommissioning the turbine is both a prudent and timely measure to ensure public safety," the company said on its website.
The facility had cut carbon emissions by about 13 million kilograms in its lifetime, equivalent to the carbon dioxide absorbed by around 560,000 trees in a year, HK Electric said in a statement.
Hong Kong is heavily dependent on fossil fuels including natural gas and coal for electricity, with renewable energy accounting for about one percent.
Offshore wind farms have been proposed by the financial hub's two power companies, but the projects have been put on hold due to high costs.
Hong Kong has a target to achieve carbon neutrality before 2050.