A final vote count showed that Hamas had won 40 of the 81 seats making up the student general assembly of al-Najah University in Nablus.
Fatah won 34 seats while the Democratic and Popular Fronts for the Liberation of Palestine (DFLP) and (PFLP) won two seats each in Tuesday's vote.
The Palestinian Democratic Initiative, led by former presidential candidate Mustafa Barghouthi, received one seat.
Supporters of the Islamic Jihad organisation won two seats.
In last year's elections, Fatah won 38 seats as against Hamas' 36.
Journalist Sedqi Mousa attributed the success of Hamas to the "weakness and incompetence of the Fatah-led student council".
"Last year many students were moved by the death of Yasser Arafat and cast their votes in favour of Fatah. Moreover, the Islamic student bloc has been able to convince new students of the authenticity and veracity of the Islamic line."
After the announcement of the election results, hundreds of Islamist students and Hamas supporters marched to downtown Nablus shouting "God is great" and "Jerusalem in our eyes".
Others shouted "forward to parliament," referring to Hamas' decision to take part in the Palestinian parliamentary polls, scheduled for 25 January.
Al-Najah is the largest university in the West Bank, with as many as 14,000 students.
Many observers consider student elections in the occupied territories as a barometer reflecting the political currents in the Palestinian street.