Background: The waiting time (WT) for a phlebotomy is directly related to patient satisfaction with a health service. However, the processing time varies widely depending on the type of patients. Monitoring of the WT alone may not enable an effective evaluation of the lean performance of the medical staff for patients with different characteristics. The objective of this study was to use process cycle efficiency (PCE) to assess the performance of an intelligent tube preparation system (ITPS) which automatically labeled test tubes and conducted patient rerouting for phlebotomy services, and to interpret the WT during peak hours. Methods: Three time periods were used. The baseline period was from 1 July to 31 July 2014. Phase 1 was after the establishment of the ITPS, with patients ≥80 years old being rerouted. In phase 2, patients ≥78 years old were rerouted. Those data were recorded with a calling system and ITPS, respectively. Results: PCE was significantly improved from 12.9% at baseline to 51.1% (p < 0.001) in phase 1 and 53.0% (p < 0.001) in phase 2. The WT of 16.9 min at baseline was reduced to 3.8 min in phase 1 (p < 0.001), and 3.6 min in phase 2 (p < 0.001). Moreover, the results showed that a WT < 10 min was consistent with a PCE ≥ 25%. Conclusions: Establishing an ITPS for phlebotomy can significantly increase PCE and shorten the WT. Furthermore, the PCE ≥ 25% could be a good assessment reference for the management of appropriate human resources for phlebotomy services, although it is a complex parameter.