Transport operator system TEİAŞ, applies penalty to the customers which are damaging the system. The source of the penal clause as a rule, is the system application contract. However the parties didn’t have signed a system application contrat, the penal clause will be applied according to the Procedure Directive. To implement a penalty clause according to the system application contract of TEİAŞ, a caution must be sent and an additive term should be granted for the caution to end in accordance with the article 10 of the contract. According to the Procedure Directive, the issue of the application or not of a penalty clause is controversial. No warning clause is predicted in the Procedure Directive. This lacuna in the Procedure Directive must be filled with the use of the system application contract and the caution condition should be applied in this case. As TEİAŞ and its customers are legal entities of private law, and as their relationship are private law relationship, the authorized court for the lawsuits concerning the cancellation of the penalty clause in accordnace of the Procedure Directive are the judicial courts.