The minimum requirement for uncertainty estimation is to use only intermediate precision (R_w), especially for measurands lacking a reference measurement system such as thyroid functions tests (TFT). In this study, measurement uncertainty (MU) for TSH and FT4 from long-term internal quality control (IQC) data was estimated while reference change values (RCV) were calculated from estimated MU. Furthermore, intermediate precision (R_w) was used to establish appropriate risk-based QC frequency. Twenty fore months of third party IQC data were collected retrospectively, on the Abbott ARCHITECT i1000sr analyzer from INSTITUT PASTEUR OF MSILA laboratory, ALGERIA. The MU, RCV and sigma-metric were estimated simply from the intermediate precision (R_w), while a nomogram relating sigma performance to run size was used to establish QC frequency. The MU for the TSH and FT4 was 12% and 8% respectively. The U _one-sided for the TSH and FT4 was 10%, 6.6% respectively. MU and U _one-sided of TSH and FT4 met quality requirements for permissible uncertainty (pU %) and allowable total error (ATE %). When monitoring thyroid replacement therapy, an upward minimum change (RCV) of 54% and 22% or a downward of 35% and 18% in serum TSH and FT4 respectively, would be considered significant. Optimal QC strategy for serum TSH was selected to run 4 QC materials every 190 patients sample and to use a multi-rule (1_3s/2_2s/R_4s/4_1s). Our results suggest that MU estimation from long-term IQC alone may be acceptable for TFT to assist physician in results interpretation and to establish appropriate QC frequency.