The properties would be clustered in north, northwest and southwest Houston in Independence Heights, Braeburn Glen and Langwood neighborhoods.
Houston City Council voted in October to fund the buyouts with $10.7 million in federal grant money.
The 39 buyouts will be funded by money the city received after two floods in 2015, including the Memorial Day floods.
The buyouts are separate from an ongoing $20 million effort by the county to buy out roughly 200 homes flooded during Hurricane Harvey.
They also are separate from the county’s application approved by Commissioners Court in November for $17 million to buy out 106 homes, and another 2016 federal grant to buy out 41 properties approved in October.
The Harris County Flood Control District began administering a buyout program in the mid 1980s, and since has bought out more than 3,000 homes