As the final stage of EEC-Turkey Association Agreement (Ankara Agreement-1963), the Customs Union between Turkey and the European Union was established on 1 January 1996 with the Decision No. 1/95 of the EC-Turkey Association Council. With the establishment of the CU, Turkey and Turkish industry have got into a reform process. While Turkish governments have fulfilled their obligations for the smooth functioning of the CU, Turkish industry has adapted itself with EU market conditions in order to compete with industries of EU member states. With the CU, the parties have had free access to markets of each other for industrial goods and exportation of Turkey to the EU as well as its importation from the EU have increased dramatically. In Turkey, production and consumption have multiplied, technological developments have been ensured, competitiveness has increased, foreign direct investment has escalated, and economic growth and development has been provided. However, the CU whose provisions were designed as if it would exist for 5 years has caused significant problems which were not taken into account or attached importance before the ACD No. 1/95 was signed. This study examines certain problems of Turkey within the scope of negotiating free trade agreements with third countries, which is one of the obligations of Turkey in order to align Common Commercial Policy of the EU. Although some of the problems correlated with FTAs have existed since the establishment of the CU, they mainly started to draw attention in recent years after the shift in foreign trade policy of the EU. As a result, unfair competition conditions have occurred for Turkey and smooth functioning of the CU has been disturbed. Within this context, in the study, the reasons of FTA problems of Turkey within the CU will be revealed and their economic results on Turkey will be evaluated. In order to handle these problems, the possible practices of Turkey within the existing legal structure will be assessed and then, alternative solutions to these problems will be discussed under the ongoing or new initiatives.