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

conf/neo4j-wrapper.properties

In order to specify the parameters, add a line for the additional java arguments to read.

# Java Additional Parameters
wrapper.java.additional.1=-Dorg.neo4j.server.properties=conf/neo4j-server.properties
wrapper.java.additional.2=-Dlog4j.configuration=file:conf/log4j.properties
wrapper.java.additional.3=-agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=5005 -Xdebug-Xnoagent-Djava.compiler=NONE-Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=5005

which will start a Neo4j server ready for remote debugging attachement at localhost and port 5005. Use these parameters to attach to the process after starting the server from Eclipse, IntelliJ or your remote debugger of choice.