A binary file is a file whose content must be interpreted by a program or a hardware processor that understands in advance exactly how it is formatted. That is, the file is not in any externally identifiable format so that any program that wanted to could look for certain data at a certain place within the file. A progam (or hardware processor) has to know exactly how the data inside the file is laid out to make use of the file.
In general, executable (ready-to-run) programs are often identified as binary files and given a file name extension of ".bin". Programmers often talk about an executable program as a "binary" and will ask another programmer to "send me the binaries." (A synonym for this usage is object code .) A binary file could also contain data ready to be used by a program.
In terms of transmitting files from one place to another, a file can be transmitted as a "binary," meaning that the programs handling it don't attempt to look within it or change it, but just pass it along as a "chunk of 0s and 1s," the meaning of which is unknown to any network device.