"This is an important site that was even featured in a propaganda video by the Iranian regime in the past," military spokesman Brigadier General Effie Defrin told journalists.
He was likely referring to footage aired by Iran's Revolutionary Guards earlier this year showing what it described as a new underground missile facility.
"It was struck and the senior officials associated with it have also been eliminated," Defrin said, adding that "dozens of other such sites have also been destroyed".
The military said the site contained "storage tunnels for surface-to-surface missiles and cruise missiles as well as multiple launch shafts".
Iranian media reported strikes on Lorestan province, where Khorramabad is located, on Saturday.
Earlier on Saturday Israel said its air strikes on Iran, which began in the early hours of Friday, have so far killed more than 20 Iranian army and Revolutionary Guards commanders, including armed forces chief Mohammad Bagheri.
The strikes have also killed nine nuclear scientists and experts, the military said.
Iran said at least 78 people have been killed.
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