Phase-coherent transport manifests itself in various quantum phenomena. Universal conductance fluctuations (UCF) are one of them. Here, we report the detailed study of dephasing of electronic wavefunction by analyzing UCF and weak antilocalization in a device, made by exfoliation from a bulk insulating topological insulator single crystal (Bi1Sb1Te1.5Se1.5). From the parallel magnetic field measurement, we proved that the quantum phenomena in our sample are caused by surface Dirac electrons. Our sample showed very slow dephasing of electronic wavefunction, which has rarely been observed in topological insulator materials. This kind of dephasing indicates the presence of electron–hole charge puddles in our system. The RMS amplitude of the UCF is also surprisingly higher (13 e2h) than the universal value of the conductance fluctuation (e2h) and the fluctuations persist in our sample until the temperature as high as 20 K and above. We also show that the shape of the flake has a significant impact on the prefactor, α, of the Hikami–Larkin–Nagaoka equation. Moreover, the formation of Aharonov–Bohm loops of different areas is responsible for UCF. By analyzing the fast Fourier transform of the UCF data, we have obtained these Aharonov–Bohm loops which are contributing to the UCF.