Rutte’s centre-right VVD Party won 31 out of 150 seats, polls suggest.
His party came far ahead of the next three parties, including Geert Wilders’ anti-immigration Freedom Party (PVV), the Christian Democrats and the D66 Party, which each got 19 seats.
Mr Wilders’ party had been leading in opinion polls but support for the party appeared to slip in recent days.
Voter participation in the general election was high – and experts say the final turnout may reach 80%.
Analysts say a high turnout may have benefited pro-EU and liberal parties.
A campaign leader for Mr Rutte’s party said the voters had given “trust again” to the VVD.
Many had been watching the vote in the Netherlands closely, as an indication for how populist parties may fare in other elections in EU countries.
France goes to the polls next month to elect a new president while Germany is due to hold a general election in September.
As parliamentary seats are allocated in exact proportion to a party’s vote share, the VVD party will need to go into coalition with other parties.
The VVD will need at least three other parties before it can secure a majority.