Myrrh essential oil (MEO) is widely used as remedies for the different human ailment in different parts of the world. The misuse of this natural product in higher doses may lead to fever, inflammation, and liver and kidney problems. In this study, we performed the acute and subacute toxicity analysis of MEO in mice model after subcutaneous injection and evaluated the safe dose to prevent the possible risk and side effects. Initially (first phase study) higher dose of MEO (20, 40, and 80 μL) was injected, and later in the second phase study lower dose of MEO (1, 5, and 10 μL) was injected for three days in each group of mice. Blood samples were taken for the investigation of hematological parameters and activity of various enzymes. The liver, kidney, spleen, lungs, and heart were excised for histological study. The body weight and skin abnormalities were also evaluated. In the first phase study, the mice showed granuloma formation at the site of injection. The liver showed dilated sinusoids and enlarged central vein. In the spleen the distinction between red and white pulp was lost. The kidney showed the degeneration of glomerulus. The enzyme activity and body weight were also decreased by the higher dose. The WBC count also increased nearly by twofold. Pruritus and self-trauma were also evident. Later in the second phase study, the skin abnormalities (granuloma) and damage in the structure of tissue (in liver, spleen, and kidney) were absent along with no change in enzyme levels, blood parameters, and body weight compared to the control. The MEO was toxic to liver, spleen, and kidney in the higher doses. The safe volume of MEO useful for various studies in mice was evaluated. The safe use of MEO should be assured, it should not be misused, being considered as a natural remedy, and there should be awareness of its toxicity and side effects.