If you are in Tokyo and you have only one day to visit Kyoto, then take a bullet train (Shinkansen). It takes one hour and 12 minutes one way.
Kyoto from Tokyo Bullet train
Shinkansen bullet train runs almost every 5 minutes during day time. So you never miss one. There are three types of categories of Shinkansen. You should take Nozomi Express and avoid Hikari and Kodama. Hikari and Kodama stops at many stations between two cities, and takes more time than Nozomi.
If you take a Nozomi departing from Tokyo at around 7:30 am, you can arrive at Kyoto Station by 10:00 am. You can leave from Kyoto Station to Tokyo, after dinner.
One day model plan
8:00 am: Leave from Tokyo by Shinkansen Nozomi Express 207
10:15 am: Arrive at Kyoto Station
10:15 am: Join in the “Private Kyoto Tour” or a similar tour from Kyoto Station
Go around Kyoto with a guide for 8 hours
18:15 pm: End of the tour at Kyoto Station, take dinner around Kyoto Station
19:21 pm: Depart from Kyoto Station by Shinkansen Nozomi Express 444 heading Tokyo
Tours in Kyoto
If you are familiar with transport in Kyoto, you can visit various places by yourself. Nowadays, Google Map can tell you how to reach to next destination, although the bus network is very complicated in Kyoto.
If you are not very sure where you go, or how to take public transport, then consider joining in a package tour. There are so many Kyoto highlight tours for a day. Some tours have fixed itineraries, while others are designed to allow you to consult with your guide and decide where you want to go. Some are by private cars while others use public transport or on foot.
Link: Hidden gems of Kyoto provides full of information about tourist destinations in Kyoto.