The Federal Constitutional Court in the western Germany city of Karlsruhe threw out the woman's appeal because she was "unable to give a coherent account of how her fears would come about."
"The overwhelming scientific opinion is that the experiments carried out at CERN (the European Organisation for Nuclear Research) present no dangers," the court ruled.
CERN scientists are looking to the Large Hadron Collider (LHC) to mimic the conditions that followed the Big Bang and help explain the origins of the universe.
Housed inside a 27-kilometre (16.8-mile) tunnel straddling the Franco-Swiss border, the collider was started with great fanfare in September 2008, only to break down after nine days for the next 14 months.
It was shut down again in December, this time to ready it for collisions at unfathomed energy levels which began last month.
The scientists' holy grail is to find a theorised component called the Higgs Boson, commonly called the "God Particle", which would explain how particles acquire mass.
The woman had argued that Germany — as a member of CERN, or the European Organisation for Nuclear Research — should be obliged to intervene and ensure that the amount