The drone has been taken in for further inspection by the military on Monday.
Earlier on Sunday, the official of Kibbutz Zikim near the southern city of Ashkelon informed the local residents that two suspicious objects had been seen on the community’s territory.
The IDF has not specified the geographical location of where the UAV was brought down.
There was no comment from Gaza. Its militant Hamas leaders are known to have developed a drone program with Iranian help. The drones are typically used for reconnaissance along the Israeli-Gaza border and it's unclear if they have potential to carry out attacks.
The incident comes amid low-level tensions along the border as Israel and Gaza are still trying to maintain an informal truce between them following May's cross-border deadly flare-up.
Meanwhile, on Friday some 7,000 Gazans took part in the weekly March of Return demonstrations along the border with Israel. The protesters hurled rocks and explosive devices at the security fence, prompting the military to respond with crowd dispersal measures.
Associated Press contributed to this report