GPS time series consists of a linear trend, harmonic signals, probable offsets and also noise which is described as a stochastic part. Because of various applications of GPS time series such as plate tectonics, crustal deformation and earthquake dynamics studies, these time series should be modeled with high accuracy. For this purpose, systematic effects in functional model should be determined with high accuracy. In this paper the effect of earthquakes is also considered in the functional model in addition to mentioned behaviors. Because earthquakes cause crustal deformations, their effects can be observed in the shape of offsets (as coseismic effects) and (or) rate changes (as coseismic or postseismic effects) in the time series. Neglecting these effects lead to biased estimation of noise amplitudes. To discover the effect of earthquakes, a manual solution is used for each station. Effects are detected graphically by comparison of behavior of time series and epoch of occurred earthquakes in the region. The earthquakes which considering their effects, lead to the best fitting of functional model to time series, are selected as effective ones. Because the Alborz range is the most seismically active region in the Northern Iran, 25 permanent GPS stations with the time span between 2005 and 2013 in this area are selected for this study. Analysis of time series indicates similar behavior of time series with the same offset times and common earthquake effects for most stations (also for those which are located in far distances from epicenters). This result means that systematic effects may propagate from one station to the others during the processing and the network adjustment. Furthermore, noise analysis of time series using least squares (co)variance components estimation method, shows that neglecting seismic effects can result in the presence of random walk noise in 88%,12% and 60% of north, east and up components, respectively. However, considering the seismic effects causes positive estimation of variances of random walk noise in 12%,12% and 36% of north, east and up components, respectively. Finally, due to similar behavior of time series, a reprocessing of them could be suggested.