SQLite Forum

Proposed slightly-incompatible change to date-time functions
There are a number of issues with this.  

The first is that internally the datetime value is maintained in "milliseconds since the julian epoch" as a 64-bit integer.  This means that there is no way to generate output with more resolution than a millisecond.

Secondly, even though Windows internally maintains time to the hun (hundreds of nanoseconds) the call used to access that time has an update frequency of a tick (about 16 milliseconds).  Although you can change the system call used to get the time so that it obtains the "precise" time rather than the tick time, it will still not be used internally by SQLite to any more than millisecond resolution.

Although Unix systems will return the tod with a nanosecond resolution, the granularity is up to the OS, and in any case, only millisecond resolution is used internally.