Turkey, a key country on the migrant route to Europe, is central to Merkel's diplomatic efforts to reduce the flow of incoming people.
The chancellor's visit comes days after a renewed round of criticism by EU officials about Turkey's lack of efforts to curb the number of migrants making their way to Europe.
At the same time, Turkey faces mounting pressure to open its border to up to 35,000 Syrians who have massed along the frontier fleeing an onslaught by government forces.
Turkey, home 2.5 million Syrian refugees, says it has reached its capacity to absorb refugees but has indicated that it will continue to provide refuge.
Turkey agreed in November to fight smuggling networks and help curb irregular migration. The EU has pledged 3 billion euros (£2.3 billion, $3.3 billion) to help improve the condition of refugees.
But since the deal, EU officials have denounced Turkey on more than one occasion, arguing that the country was not doing nearly enough to help curb the flow of migrants making their way to Europe.
On Saturday, European Commissioner for enlargement Johannes Hahn, warned that Turkey needed to show results in the coming weeks, before a European summit on February 18.
REUTERS/Darrin Zammit Lupi
Hahn also warned that if Turkey failed to dramatically cut the number of migrants reaching Greece within weeks, the pressure for more border closures and fences would grow.
In January alone, over 68,000 crossed the Aegean Sea into Greece, according to the United Nations High Commissioner for Refugees (UNHCR) and over 360 people lost their lives trying to reach Europe.