The objective of this work was to map population of common juniper (Juniperus communis L.) in the territory of Slovak Republic. Common juniper is not protected by Slovakian law or the authorities; therefore, there is no law to preserve these plant populations. Biotopes of common juniper consist of light- to heavy-density trees and shrubs. The expansion of its habitat is also connected to human involvement. The loss of juniper naturally in observed plants is caused by a change in land use, loss of feeding pastures for cattle and sheep, and eutrophication of the environment. The current study was focused on monitoring the population of this plant species in the years of 2018–2020, the isolation of essential oils, and the identification of qualitative and quantitative characteristics. It was confirmed that juniper berries usually contain from 0.5 ± 0.05 to 1.8 ± 0.06%, usually 1.2 ± 0.16%, volatile oil depending on geography, altitude, ripeness, and other factors. Volatile oil is made up mostly of monoterpenes, mainly α-pinene (from 37.60 ± 2.23 to 61.00 ± 0.60%), β-myrcene (from 8.03 ± 2.02 to 10.56 ± 0.05%), and sabinene (from 3.50 ± 0.30 to 22.0 ± 0.96%). The dendrogram was constructed after a hierarchical cluster analysis based on the essential oil substances, which showed four different confirmed chemotypes. The essential oil is widely used in medicines, perfumes, insect repellents, insecticides, shoe polish, and in microscopy as a clearing agent of an immersion oil. The quality and chemotypes of juniper berries are very important for the Slovak national beverage “Borovicka” and the distillery industry on a whole in this country.