"Hundreds of residents in the flooded areas around Sheikh Radwan storm water lagoon have evacuated their homes," the UN agency for Palestinian refugees said, referring to a northern district.
Some 100,000 Palestinians throughout Gaza remain homeless three months after a ceasefire ended a bloody 50-day war between Israel and Hamas militants, with reconstruction yet to begin.
While no casualties have been reported from the flooding, UNRWA said it was supplying "emergency fuel to municipalities, water, sanitation and health facilities".
Robert Turner, its director of operations in Gaza,said the agency was "very concerned about such severe storms this early in the season and on the back of unprecedented damage and destruction" from the war.
Signup to our newsletter and follow us on Facebook and Twitter!
Thousands of Gazans were displaced last December after torrential rain hit the coastal territory, UNRWA said.
"Such devastation exacerbates the already poor humanitarian situation for refugees and non-refugees in Gaza, which is dealing with the aftermath of a recent conflict and an acute fuel and energy crisis," it said.
Little construction materials have entered Gaza following a UN-brokered deal under which Israel eased an eight-year blockade of Gaza.
According to a foreign diplomatic source, the mechanism for delivering materials has "taken longer than anticipated" to launch.