Mogherini "will be in Ramallah this afternoon to meet president Mahmud Abbas and foreign minister Riyad al-Malki", the ministry said in a statement.
It also said Mogherini would travel to Ashdod, a southern port town close to the border with the Gaza Strip, along with Israeli Foreign Minister Avigdor Lieberman, and visit a home hit by a rocket attack.
A Gaza rocket struck the town earlier on Tuesday, just hours after Israel agreed to abide by an Egyptian truce that was rejected by Hamas.
Israel's Operation Protective Edge, intended to stamp out militant rocket fire, had killed 186 people in Gaza by late Monday - exceeding the toll in the last similar flare-up of violence in 2012. A UN reported issued on Sunday said that 77 percent of those killed were civilians.
Mogherini is expected to meet Israeli Prime Minister Benjamin Netanyahu and President Shimon Peres on Wednesday, as well as visit the Yad Vashem Holocaust memorial.
A 41-year-old who has only been in government since February, Mogherini is seen as a possible pick for a European Commission post or to be the EU's next foreign policy chief.