In the Turkish capital, police clashed with demonstrators as they tried to stop traffic, making a number of arrests and leaving several injured.
In Istanbul, large crowds shouting anti-government slogans lit a huge fire as they made their way to a cemetery for the burial of 15-year-old Berkin Elvan.
Scuffles broke out when police tried to prevent a group of protesters from gathering on the city's Taksim Square, the epicentre of last June's mass protests.
Elvan, who died in an Istanbul hospital on Tuesday after 269 days in a coma, was hit on the head by a tear gas canister while going to buy bread during the protests against Prime Minister Recep Tayyip Erdogan that gripped Turkey in June.
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"Berkin's murderers are the AKP police," protesters shouted in Istanbul, referring to Erdogan's ruling Justice and Development Party (AKP).
"The rage of mothers will suffocate the killers," screamed others as they marched through the streets after Elvan's funeral.
Elvan's story became a symbol for many Turks of the heavy-handed police tactics against mass anti-government demonstrators in June, a major challenge to Erdogan's 11-year-rule.
The prime minister has vowed to step down if the AKP, in power since 2002, loses local elections on March 30 that are seen as a key test of his popularity after last year's unrest and an ongoing graft probe that has ensnared key AKP allies.
Government spokesman Bulent Arinc said Turkey had been in mourning since Elvan's death.