The vote, which took place on Wednesday, will determine whether the ruling Botswana Democratic Party will lengthen its 58 years in power.
Some polling officers say stations were busy right up until they closed.
Independent Electoral Commission polling officer, Gomotsang Dintle, said, "today was a bit hectic because there were people flowing in the whole day. We opened the polls at 06:30 but people were there until we closed."
63-year-old Mokgweetsi Masisi is seeking a second and final term in office.
His main opponent is Duma Boko of the Umbrella for Democratic Change party.
Vote counting is underway and results are expected to be given in the coming days.
Financial issues have been at the forefront of many voters' minds, as the county's economy has been hard-hit due to a fall in demand for diamonds, which Botswana is strongly reliant upon.
