The impact of space weather events on satellite-based technologies (e. g. satellite navigation and precise positioning) is typically quantified on the basis of the total electron content (TEC) and temporal fluctuations associated with it. GNSS (global navigation satellite systems) TEC measurements are integrated over a long distance and thus may include contributions from different regions of the ionised atmosphere which may prevent the resolution of the mechanisms ultimately responsible for given observations. The purpose of the experiment presented here was to compare TEC estimates from EISCAT and GPS measurements. The EISCAT measurements were obtained along the same line of sight of a given GPS satellite observed from Tromso. The present analyses focussed on the comparison of temporal fluctuations in the TEC between aligned GPS and EISCAT measurements. A reasonably good agreement was found between temporal fluctuations in TEC observed by EISCAT and those observed by a co-located GPS ionospheric monitor along the same line of sight, indicating a contribution from structures at E and F altitudes mainly to the total TEC in the presence of ionisation enhancements possibly caused by particle precipitation in the nighttime sector. The experiment suggests the great potential in the measurements to be performed by the future EISCAT 3D system, limited only in the localised geographic region to be covered.