"We need to improve on the alignment on foreign policy and security policy, it`s never been so low and this is a problem for the European Union, but it is mainly a problem for Turkey," she told a news conference in the Turkish capital.
The visit by Mogherini, Enlargement Commissioner Johannes Hahn and Humanitarian Aid Commissioner Christos Stylianides is aimed at giving new impetus to the relationship, including urging closer cooperation against Islamic State and pressing Ankara not to undermine EU sanctions on Russia.
It comes a week after Russian President Vladimir Putin`s trip to Turkey, during which Moscow announced it was scrapping the South Stream gas pipeline project and named Turkey as its preferred partner for an alternative.
Mogherini said the EU would not be drawn into a battle with Russia for influence over Turkey.
"It would be good if in the future we create more areas for cooperation rather than competition (with Russia) but Turkey is definitely out of this game, if there is a game in this sense," she said.
Mogherini said earlier that European member states needed to work closely with international partners such as Turkey to stop foreign fighters travelling to the Middle East and joining radical Islamist groups.
Thousands of EU citizens are thought to have travelled to Syria and Iraq to join radical groups including ISIL, many transiting through Turkey, which has faced criticism for failing to control its 1,200-km border with the two.
Officials in Ankara have in turn accused European nations of doing too little to stop would-be jihadists at source, while expecting Turkey to pick up the slack. A Turkish official said some 1,150 people had already been intercepted and sent back.