Kristen Brekke, 19, of Cardiff, Forhad Rahman, 21, of Gloucestershire, and Adeel Ulhaq, 20, of Nottinghamshire, denied assisting another in the preparation for committing terrorist acts.
Judge Rebecca Poulet QC discharged the jury at London's Old Bailey on Tuesday.
A new trial will be held in future.
It is alleged the three men helped Aseel Muthana, 17, go to Syria in 2014 to join Islamic State fighters.
The trial of three men accused of helping a Cardiff teenager travel to Syria to fight for Islamic State has been halted.