You build the target binary using a special version of gcc:

    3) Instrumenting programs for use with AFL
    ------------------------------------------

    Instrumentation is injected by a companion tool called afl-gcc. It is meant to
    be used as a drop-in replacement for GCC, directly pluggable into the standard
    build process for any third-party code.

    [...]

    The correct way to recompile the target program will vary depending on the
    specifics of the build process, but a common approach may be:

    $ CC=/path/to/afl/afl-gcc ./configure
    $ make clean all

    [...]