One of the men was accused of collaborating with Israel and the others had been found guilty of murder.
The man executed for collaborating with Israel is the first to be hanged for the offence since two similar executions last July.
Under Palestinian law, executions are meant to be approved by the Palestinian president.
But since the split between Hamas-controlled Gaza and the Palestinian-Authority-run West Bank, Hamas does not recognise the authority of President Mahmoud Abbas.
The BBC's Middle East correspondent Kevin Connolly says it is impossible to assess the quality of the evidence presented against the three men who have been executed.
Court proceedings in the Gaza Strip are not held in public, and defendants are identified only by their initials, so it can be difficult event to match announcements of executions even with previous news of arrests or convictions, our correspondent says.
It is not even possible to know what specific charges the executed men faced, he adds.
Israel's intelligence services recruit informers to gather information about possible targets for militants and help block attacks.