Step 1 :- GO to My Apps App in iTunes Connect
Here you can see your all app which are currently on Appstore.
Step 2 :- Select your app which you want to delete.(click on app-name)
Step 3 :- Select Pricing and Availability Tab.
Step 4 :- Select Remove from sale option.
Step 5 :- Click on save Button.
Now you will see below your app like , Developer Removed it from sale in Red Symbol in place of Green.
Step 6 :- Now again Select your app and Go to App information Tab. you will see Delete App option. (need to scroll bit bottom)
Step 7 :- After clicking on Delete button you will get warning like this ,
Step 8 :- Click on Delete button.
Congratulation , You have Permanently deleted your app successfully from appstore. Now , you cant able to see app on appstore aswellas in your developer account.
Note :-
When you have selected only Remove from sale option you have not deleted app permanently. You can able to make your app live again by clicking on Available in all territories option Again.