Clinical diagnosis requiring central facilities and site visits can be burdensome for patients in resource-limited or rural areas. Therefore, development of a low-cost test that utilizes smartphone data collection and transmission would beneficially enable disease self-management and point-of-care (POC) diagnosis. In this paper, we introduce a low-cost POC diagnostic strategy which integrates 3D design and printing of microfluidic POC device with smartphone-based disease diagnosis in one process as a stand-alone system, offering strong adaptability for establishing diagnostic capacity in resource-limited areas and low-income countries. We employ smartphone output (AutoCAD 360 app) and readout (color-scale analytical app written in-house) functionalities for rapid 3D printing of microfluidic auto-mixers and colorimetric detection of blood hemoglobin levels. The auto-mixing of reagents with blood via capillary force has been demonstrated in 1 second without the requirement of external pumps. We employed this POC system for point-of-care diagnosis of anemia using a training set of patients (n = 16 and n = 6), which showed consistent measurements of blood hemoglobin levels (a.u.c. = 0.97) and comparable diagnostic sensitivity and specificity, compared with standard clinical hematology analyzer. Capable of 3D fabrication flexibility and smartphone compatibility, this work presents a novel diagnostic strategy for advancing personalized medicine and mobile healthcare.