There are several ways to reach Sakamoto and Mount Hiei.
By bus
There are occasional direct buses from Kyoto station directly to the top, taking about 1.5 hours and all departing in the morning. Schedules are severely curtailed in the winter.
By train
From Kyoto, the JR Kosei line goes directly to the Hieizan-Sakamoto station which is a 1,200 meter walk from the Sakamoto Cable Car or the trailhead to climb Mount Hiei on foot. Alternatively, take the Keihan Main Line to Demachiyanagi and transfer to an Eizan train to Yase-Hieizan-guchi å «ç¬æ¯å¡å±±å£. From here the Eizan Cable Car makes the trip to the top of Mount Hiei for ¥530/1040 one-way/return incl. the ropeway: ¥820/1640 one-way/return, every 30 minutes daily from 8:30 to 17:30 or longer, schedules vary a bit depending on the season. The last leg of the trip to the summit is a 3-minute ride on a ropeway, which departs at intervals of 10-20 minutes between 9 am and 6 pm.
Alternatively, you could also take the Keihan Line to Sanjo Station and transfer to the Tozai Line bound for Hamaotsu Station in Otsu. From Otsu, you can take the JR Kosei line or Keihan Ishiyama-Sakamoto line to Sakamoto, although the Keihan station the last station on the line is more centrally located. The Hiyoshi Taisha shrine and the cable car to Mt. Hiei are about 15 min away on foot, both fairly well signposted.
Be careful: there are two different cable-cars up the hill, each ran by a different company. So, if you buy a two-way-ticket from one company, you cannot use this for the other railway and you'll need to buy a new ticket.