In order to configure the Neo4j server for remote debugging sessions, the Java debugging parameters need to be passed to the Java process through the configuration. They live in the conf/neo4j-wrapper.properties file.
In order to specify the parameters, add a line for the additional Java arguments like this:
dbms.jvm.additional=-agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=5005
This configuration will start a Neo4j server ready for remote debugging attachement at localhost and port 5005.
Use these parameters to attach to the process from Eclipse, IntelliJ or your remote debugger of choice after starting the server.