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 costs, schedules, performance, and risk implications.
The functional architecture is used to support functional and performance test development. It also supports the 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.
SEBok Definition: A functional architecture is a set of functions and their sub-functions that defines the transformations of input flows into output flows performed by the system to achieve its mission.
During the Functional Analysis and Allocation step, the functional requirements identified in the Requirements Analysis step are decomposed 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 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
- Website: SEBok – Guide to the System Engineering Body of Knowledge