This study aims to develop a practical algorithm for utilizing smartphone-based thermal imaging (SBTI) in the perioperative setting and to establish a standardized evaluation method for objectively assessing SBTI images for cutaneous perfusion of pedicled flaps in the face, head, and neck. This prospective conducted study, integrated SBTI into the assessment of 16 patients undergoing reconstructive surgery for face and neck defects. Thermal images were captured at four timepoints: after marking (T1), after flap elevation (T2), upon completion of surgery (T3), and 24h postoperatively (T4). The flap areas were divided into three flap zones and graded based on temperature differences (ΔT), with a grading system where grade 1 indicated perfect perfusion and grades 2 to 5 indicated increasing perfusion impairment. 6 male and 10 female patients aged 64-93 years (mean 78.5 years) undergoing reconstructive pedicled skin flap surgery for facial and neck defects (1 × 1cm to 11 × 8cm) due to diagnoses of malignant cutaneous lesions were investigated. Intraoperative assessments indicated good perfusion across flaps. One postoperative dehiscence occurred in an 83-year-old male with a cervical advancement flap, correlated with a significant temperature difference (ΔT > 4°C) intraoperatively. Statistical analysis revealed a strong positive correlation (p = 0.0003) between clinical assessment grades and ΔT values between specific flap zones at T3. SBTI is an easy-to-apply, low-cost, real-time and reproducible technique for indirect perfusion assessment in pedicled skin flaps of the head and neck region. Further studies are needed implementing this methodology in large and free flaps.