In the early stages of the establishment of an innovative enterprise, tax stimulation is an effective means of saving working capital that can be used for other purposes in order to develop business. The rational construction of the accounting system of an innovative enterprise helps to optimize its costs and tax calculations. The article shows that a startup is a form of innovation; the fundamental factors of the effectiveness of a startup company were identified, including integrity, honesty, and transparency of business, market knowledge and a «raw» product testing, reliable partners, effective staff with intrinsic motivation, high project ambitions, continuous development. The peculiarities of taxation of innovative activity were investigated, in particular, the activity of startup companies. The use of tax breaks for startup companies in the early stages of the establishment of an innovative enterprise is an effective means of saving working capital that can be used for business development. The article identifies the main types of tax stimulation (tax benefits) of startup companies, which include the following: tax holidays, tax innovation benefits, accelerated depreciation, reduction of the tax base by the amount of innovative capital expenditures (investment discount), reduction of tax liabilities of the income tax (simple (voluminous) and incremental tax credit). It was defined that the accounting nature of tax stimulation for startup companies, which contributes to the development of the startup company as a whole, provides optimization of its costs and tax calculations, and development of appropriate accounting support. All this will help to optimize the costs of the economic activity of an innovative enterprise and to optimize the tax payments of a startup company to the state.