An Israeli F16 fighter jet conducted the strike Tuesday night or Wednesday morning, hitting the facility near the town of Khan Younis.
Palestinian news agency WAFA reported three people were transported to a hospital in "light to moderate condition." The agency reported the two missiles damaged homes in the area.
The Times of Israel reported the airstrike came in response to a rocket Palestinians fired toward Israel hours earlier. The projectile landed in an open field near Netiv Ha'asara and caused no injuries.
On Saturday, two Hamas militants died in an Israeli airstrike on four facilities in the Gaza Strip -- two weapons manufacturing sites, a weapons warehouse and a military compound.
The strikes have accompanied protests over Trump's announcement, some of which have been violent. On Friday, two Palestinian protesters were shot dead near Gaza's border fence with Israel.