To integrate Neo4j into a Java application, you can run a Cypher query and parse the results using the Neo4j Java driver. The process involves importing the driver, connecting to a server, verifying the connection, executing a Cypher query, parsing the results, and closing the connection. You can import the GraphDatabase and AuthTokens classes from the Neo4j driver package and use them to create an instance of the GraphDatabase.driver class, passing your credentials. The executableQuery method executes a Cypher query and returns the results, which can be parsed by iterating through the records and using get to retrieve return values. Once you finish with the driver, it's essential to call close to release any resources. Neo4j GraphAcademy offers various courses, including "Using Neo4j with Java," which covers topics such as passing parameters to queries, dealing with graph data types, and managing transactions. The course is available for free and provides a comprehensive introduction to developing Java applications with Neo4j.