A Functional Architecture is an architectural model that identifies system function and their interactions. It defines how the functions will operate together to perform the system mission(s). Generally, more than one architecture can satisfy the requirements. Usually each architecture and its set of associated allocated requirements have different cost, schedule, performance, and risk implications. The functional architecture is used to support functional and performance test development. It also supports development, along with the physical architecture, of verification tasks that are defined to verify the functional, performance and constraint requirements. A system will have a functional and Physical Architecture.
During the Functional Analysis and Allocation step, the functional requirements identified in the Requirements Analysis step are decomposes and their associated performance requirements into sub functions to the point that they can be unambiguously related to the system elements or products that make up the design that flows out of a later step. The result is often called the functional architecture. 
SMC Systems Engineering Handbook, Figure 15
In the Design Loop, synthesized designs are compared with the originating architectures and allocated requirements to assure compliance or to initiate re-evaluation. Sometimes it is necessary to drive toward optimal solutions by presenting various functional views including those that depict functional relationships with existing assets to enable more thorough assessments of plausible solutions. 
AcqLinks and References:
-  SMC Systems Engineering Handbook, page 47
- Functional Software Architecture
- Functional Architecture