UN officials say the elections passed off smoothly and peacefully at 50,000 polling points across the nation, which is the size of western Europe.
The results for the Presidential elections are expected on 31 August, with the possibility of a second run-off vote on 29 October.
Human rights organisations are hoping the nation's first free elections since winning independence 46 years ago can alleviate the plight of the country's children.
Five years of civil war, a worsening health crisis and an increase in accusations of child sorcery have blighted the lives of hundreds of them in the central African state.
Martin Bell, a United Nations' Children's Fund ambassador and ex-BBC war correspondent, said, "Peace is the missing link between a violent past and a more hopeful future.
"Elections are not a panacea for all a nation's woes, but they can go a long way to restoring order and stability."
Meanwhile, dozens died in election-related violence as rampaging mobs clashed with riot police in the capital.
Decades of war
The UN has deployed its biggest peacekeeping mission - with 17,000 people - to protect the elections. It is the most expensive it has ever organised, costing $460million.
Congo has endured four decades of war and dictatorship and rebel groups still terrorise parts of the country, especially in the east.
Joseph Kabila, Congo's president, who took power after his father Laurent was assassinated in 2001, is considered the favourite of the 32 candidates standing.
After voting closed Kabila was clearly leading in one voting district in the DRC's second city, Lubumbashi.
Out of 455 ballots counted in three hours, 343 had been cast in his favour, officials said.
Kabila's challengers include former rebel leaders like Bemba who have served with him as transition leaders.
A recent UN report notes that more children under the age of five die each year in DR Congo than in China, which has 23 times the population.
Home to what UNICEF estimates is the world's largest concentration of child soldiers, the state is thought to have up to 30,000 children either fighting or living with armed forces.
Tens of thousands more live on the streets of Kinshasa and other major cities, having been thrown out by parents who either believed them to have been "possessed" or simply found them a nuisance.
These street children sleep on building sites or in shop doorways and beg, steal or do small jobs to survive.
Pressure group Human Rights Watch warned in a recent report against the "political manipulation" of Congolese street children and said the winners of Sunday's election "must begin to comprehensively address the many other abuses committed against street children".
Remi Mafou, coordinator for the French group the Network for Educators of Street Children (REEJER), warned that "both the opposition and president's circle are using them to swell the ranks of their demonstrations", which frequently degenerate into clashes between police and rival groups.
Many of the children have been forced to undergo ceremonies designed to rid them of "possession", performed by self-proclaimed pastors whose popularity is on the rise.
Several rights groups are working in the DR Congo to try to put a stop to the practice.
But they say the Kinshasa government, many of whose members are standing for re-election, is unwilling to take action against the more popular "pastors" for fear of losing votes.
More than 60,000 Congolese police were deployed to protect voting by more than 25million registered voters.
Around 1,700 international observers from Africa, Europe and the United States monitored the voting.