The purpose of this study is to reconstruct the climate variation in Japan in the first half of the second millennium. For reconstruction, daily weather record around Kyoto from the 11th century to the 16th century are used to calculate the snowfall ratio of winter and the rainy day ratio of summer. Next, regression analysis is applied on the present weather and temperature record and based on the result, the temperature changes of winter and summer are estimated. Furthermore, the influence of a climate variation is examined. The main results are as follows: 1) Winter temperature fell gradually from 1001 to 1600. Especially in 1090s, 1160s, 1260s, 1330s, 1380s and 1460s, there were substantial falls. 2) Summer temperature was rising toward the second half of the 13th century, and began to fall toward 1600, with substantial falls in 1140s, 1450s, 1560s and a remarkable rise in 1270s. 3) In the 15th century or the 13th century, the Medieval Warm Period changed into the Little Ice Age. Winter temperature of the 12th century may be higher than that of the present, and it may be lower in the 15-16th centuries than that of the beginning of the 19th century.