The objective was to compare functional outcome in patients with advanced head and neck cancer (HNC) treated with (a) surgical resection and reconstruction with microvascular free flaps (MVFF) followed by radiochemotherapy versus (b) primary radiochemotherapy (RCT) on the basis of the International Classification of Functioning, Disability and Health (ICF) from WHO. This was a cross-sectional, multi-institutional study. The outcome measures included ICF Core Sets for HNC, the EORTC-QLQ, modules c30 + hn35 and the University of Washington-Quality of life Questionnaire (UW-QOL). Analyses included descriptive statistics, ranking exercises, and regression analyses in a cumulative logit model; 27 patients were treated with MVFF and 22 with RCT. Global Quality of life scores suggested a slightly better functional outcome for the surgical approach. The majority of ICF categories (81/93, 87%) did not show a difference in functional outcome between the two treatment approaches. In the remaining 12 ICF categories, n = 3 body structures were more affected in the MVFF group, while n = 3 body functions, and n = 6 activities/participations were more problematic in the RCT group. This included oral swallowing and weight maintenance functions as well as social relationships, acquiring a job, and economic self-sufficiency. In addition, nine contextual environmental factors were more relevant to the RCT group. Both treatment approaches seemed appropriate to advanced HNC from the perspective of functional outcome. The influence of treatment modalities on the social and economic lives of cancer survivors needs to be explored further. In order to guide rehabilitation according to patients' needs, the ICF offers a multidimensional view comprising body structures, body functions, and activities and participation in life.