The development of advanced detection systems for charged particles in laser-based accelerators and the need for precise time of flight measurements have led to the creation of detectors using ultra-thin plastic scintillators, indicating their use as transmission detectors with low energy loss and minimal dispersion for protons around a few MeV. This study introduces a new detection system designed by the Institute for Instrumentation in Molecular Imaging for time of flight and timing applications at the National Accelerator Center in Seville. The system includes an ultra-thin EJ-214 plastic scintillator coupled with a photomultiplier tube and shielded by aluminized mylar sheets. The prototype installation as an external trigger system at the ion beam nuclear microprobe of the aforementioned facility, along with its temporal performance and ion transmission, was thoroughly characterized. Additionally, the scintillator thickness and uniformity were analyzed using Rutherford backscattering spectrometry. Results showed that the experimental thickness of the EJ-214 sheet differs by approximately 46% from the supplier specifications. The detector response to MeV protons demonstrates a strong dependence on the impact position but remains mostly linear with the applied working bias. Finally, single ion detection was successfully achieved, demonstrating the applicability of this new system as a diagnostic tool.