The children were accompanied by a German medical delegation headed by Jalal Othman, the administrative director of the Union of Palestinian Doctors and Pharmacists in Berlin, who arrived through the Rafah border crossing on Monday.
Othman described the injuries sustained by the children as "serious" and "complicated", adding that they cannot be easily treated in Gaza due to the crisis the medical sector is currently witnessing as a result of the siege.
"The children will be treated in cooperation with groups and hospitals across both Germany and Austria, and will be given all the medical treatment they require," he said.
He added that his union would help three additional groups of injured Gazan children receive medical treatment in Germany and Austria.
Israel's military offensive on the Gaza Strip ended with the announcement on August 26th of an open-ended cease-fire between Israel and the Palestinian militant groups of Gaza.
Almost 1,900 Palestinians, mostly civilians, have been killed since the launch of Israel's Operation Protective Edge at the beginning of July.
Some 66 Israelis - all but two of them soldiers - have also died in the mission to destroy rockets and tunnels used by the militant Islamist group Hamas.