Getting the current time (in milliseconds) from the system clock in Windows?

The easiest (and most direct) way is to call GetSystemTimeAsFileTime(), which returns a FILETIME, a struct which stores the 64-bit number of 100-nanosecond intervals since midnight Jan 1, 1601.

At least at the time of Windows NT 3.1, 3.51, and 4.01, the GetSystemTimeAsFileTime() API was the fastest user-mode API able to retrieve the current time. It also offers the advantage (compared with GetSystemTime() -> SystemTimeToFileTime()) of being a single API call, that under normal circumstances cannot fail.

To convert a FILETIME ft_now; to a 64-bit integer named ll_now, use the following:
ll_now = (LONGLONG)ft_now.dwLowDateTime + ((LONGLONG)(ft_now.dwHighDateTime) << 32LL);

You can then divide by the number of 100-nanosecond intervals in a millisecond (10,000 of those) and you have milliseconds since the Win32 epoch.

To convert to the Unix epoch, subtract 116444736000000000LL to reach Jan 1, 1970.

You mentioned a desire to find the number of milliseconds into the current day. Because the Win32 epoch begins at a midnight, the number of milliseconds passed so far today can be calculated from the filetime with a modulus operation. Specifically, because there are 24 hours/day * 60 minutes/hour * 60 seconds/minute * 1000 milliseconds/second = 86,400,000 milliseconds/day, you could user the modulus of the system time in milliseconds modulus 86400000LL.

For a different application, one might not want to use the modulus. Especially if one is calculating elapsed times, one might have difficulties due to wrap-around at midnight. These difficulties are solvable, the best example I am aware is Linus Torvald’s line in the Linux kernel which handles counter wrap around.

Keep in mind that the system time is returned as a UTC time (both in the case of GetSystemTimeAsFileTime() and simply GetSystemTime()). If you require the local time as configured by the Administrator, then you could use GetLocalTime().

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