Makeshift classrooms have been set up at Weeton Barracks while repairs are made to nearby Weeton Primary School.
The Lancashire school, hit during Storm Abigail last week, was told it would not be fit for purpose during Storm Barney. Winds peaked at 85mph on Tuesday before subsiding overnight.
About 30 soldiers helped staff and pupils move to their barracks.
The school's head teacher, Anthony Goth, praised the Army for its help.
"They were very efficient," he said. "It was very exciting - the children came into the yard as normal, and then they were frogmarched across. They thought it was great."
Storm Abigail caused widespread damage last week, leaving more than 20,000 homes without power and forcing schools to close in several parts of the UK.
The Army has stepped in to help pupils whose school has been damaged in the recent storms.