Web applications, websites and small applications are an integral part of information technology. Applications are an essential part of the information system and it is very important to run on a quality, stable and secure platform server. This thesis explains the basic concepts of Apache and Tomcat web servers and their configurations on the Windows server for the purpose of running a web application, in this thesis is used Windows Server 2012 R2. We will describe features and benefits of Apache and Tomcat web servers, and what they are used for and how they work. This thesis will describe in detail how Apache and Tomcat work independently, with mutual integration and what are the advantages of using integration. The emphasis will be on the dynamics of Apache and Tomcat's quality. The first couple of chapters deal with the theme of Apache and Tomcat itself, while later chapters mainly deal with configuration descriptions and how this configuration affects the application itself. It will also explain the importance of logs and how to use and manage them easily. Purpose of individual Apache and Tomcat configuration files will be described in depth. In this thesis it will be shown an easy way to install and launch Apache and Tomcat on the Windows server, and more complex log rotation configuration, Tomcat memory enhancement and the most important security settings of both platforms will be demonstrated. Security settings consist of enabling encrypted traffic, defense settings against DDOS attacks, and cipher strengthening. After studying the written documentation, the reader will be able to understand how Apache and Tomcat work and the basics of their configuration on a virtualized or physical Windows server.