Police spokesman Micky Rosenfeld told AFP the rocket landed in an uninhabited sector of the Negev desert, as Kerry started a three-day visit to Israel and Palestine.
Kerry is to hold a new round of talks with Israeli and Palestinian leaders on how to break a years-long impasse in direct peace negotiations.
Israeli Defense Minister Moshe Yaalon warned on Wednesday that his country would respond to any attacks on its territory and not allow its people to come under fire.
The Gaza-Israel border has been largely quiet since November when an Egyptian-brokered ceasefire ended a deadly eight-day confrontation between Israel and Hamas.
But since late February, there have been four other cases of rocket fire on Israel, three of which were claimed by Salafist militants.