Macbook Pro keyboard does not work on startup
I would reset both the System Management Controller and PRAM/NVRAM.

Reset the SMC

Instructions for resetting your System Management Controller (SMC) will depend on whether your MacBook Pro runs from a built-in battery or a removable battery.

As your question doesn't provide the exact model, use the relevant instructions below:

SMC 1 - For MacBook Pros, MacBook Airs, and MacBooks where you can’t remove the battery on your own (i.e. it's a built-in battery), here’s what you do:


Shut down your computer
Keep the MagSafe adapter (power cable) plugged in.
Press at the same time shiftoptioncontrol (on the left side of the keyboard) and the power button
Let go
Turn your computer back on with the power button.


SMC 2 - For MacBook Pros, MacBooks etc that you can remove the battery from, here’s what you do:


Shut down your computer
Disconnect the MagSafe plug (power cable) from the computer
Remove the battery
Press the power button for 5 seconds and release
Put the battery back in
Reconnect the MagSafe cord (or power cable)
Turn your computer back on with the power button


Reset your PRAM/NVRAM

Older Macs had what's called Parameter RAM (PRAM), newer Macs use Non-Volatile Random-Access Memory (NVRAM). It may be worth you also resetting this. Here’s how to:


Shut down your machine. Yes, a full shut down, not just logging out.
Press the power button and then press the commandoptionpr keys. You have to make sure you press these keys before the gray screen appears or it won’t work.
Hold those keys down until your Mac reboots again and you here the startup chime.
Let go of the keys and let your Mac reboot normally.


Note: When you log back in you may need to readjust some of your system preferences (e.g. mouse speed, time and date/timezone, etc).

Give these a go and let us know how you go.