Zero Crossing Detection of ~ 400 kHz Signal with MCU
You could use a comparator (or any opamp basically).
Since all you need to do is limit the frequency and convert the arbitrary wave into a square wave for the schmitt triggered timer capture input pin.

The most basic approach would be this absolute comparator based on a fixed reference, without any hysteresis.






simulate this circuit &ndash; Schematic created using CircuitLab

You could even use an on-chip analog comparator, if you can connect the input capture event to the comparator signal internally.

There will be caveats with this approach, but you didn't provide much details about the signal source and it's (common mode) levels.