Aleksandar Vucic's two-day visit is seen as an attempt to solve a number of issues between the two Balkan countries and boost economic ties between them despite divisions stemming from the war in the 1990s that followed the breakup of Yugoslavia.
Serbia's president visited Croatia on Monday amid protests from war veterans and festering tensions between the two Balkan rivals stemming from their war in the 90s.
President Aleksandar Vucic arrived for a two-day visit, which is seen as an attempt to solve some of Serbia's festering issues with Croatia and boost economic ties despite deep mistrust between the two neighbours.
More than 1,000 war veterans and nationalists protested against Vucic, a former fervent nationalist from the war era who now says he is a pro-EU reformer. The protesters carried Croatian flags and banners denouncing Vucic's ultra-nationalist stance during the 1991-1995 fighting that erupted when Croatia declared independence from the former Yugoslavia, triggering a rebellion by its minority Serbs.
The Croatian protesters were demanding an apology and war reparations from Serbia, which backed the minority Serb rebellion in Croatia during a conflict that killed 10,000 people.
One group of war veterans spread a huge banner reading: "Vucic, we want an apology!"
Strong security measures are in place throughout the Croatian capital for the visit, including snipers on the roofs of the houses where Vucic's motorcade was passing.
Vucic is meeting top Croatian officials, minority Serb representatives and religious leaders.
The visit was planned for last year but cancelled amid clashes between politicians over several issues.
Croatia, earlier this year, protested a Serbian exhibition about a World War II concentration camp in Croatia where tens of thousands of Serbs, Jews and Gypsies were killed by Croatia's wartime pro-Nazi puppet regime.