by the end of the day
Before the day ends. Typically refers to the end of the workday. My meeting got moved up to tomorrow morning, so I'm going to need that report from you by the end of the day.
by the end of the day
by the time when the workday is over; by the time that the sun goes down. Will this task be completed by the end of the day? We have to do all these things by the end of the day.