Muhamad Mar'i, another member of Fatah's military wing, was killed in an IDF operation in the village of Kafr Dan, near Jenin.
The man killed in Ramallah, Omar Abd al-Halim was reportedly killed after firing at IDF soldiers, who returned fire and killed him.
Halim was responsible for several shootings at Israeli vehicles, both civilian and military, and for placing explosive devices in Ramallah targeting IDF soldiers, an IDF statement said Tuesday
Palestinians opened fire at IDF special forces troops as they were leaving Ramallah. No injuries were reported.
Khaled Shwish, considered one of al-Aqsa's most prominent leaders, was arrested Monday, in a joint IDF and Shin Bet operation in Ramallah.
Shwish, 36, had been wanted by security forces for seven years for the murder of eight Israelis, and for injuring five others.
Early Tuesday morning, IDF forces arrested five Hamas and Fatah militants in the Balata refugee camp in Nablus, including Palestinian legislator Jamal Tirawi, formerly the commander of the al-Aqsa Martyrs' Brigades and the Fatah faction's spokesman in the Palestinian parliament.
IDF forces also arrested Ravia Abu-Lil, a senior member of the organization in Nablus. Palestinian sources said fire was exchanged during the arrests. No injuries were reported.
The IDF's operation in the West Bank Monday night produced 20 arrests overall. Operations against terror organization throughout the West Bank are ongoing, said the IDF statement.
Ali Waked contributed to this article