1) Obtain Color
int color = 0xff123456;
int color = getResources().getColor(R.color.my_notif_color);
int color = ContextCompat.getColor(context, R.color.my_notif_color);
2) Set the Color to the Notification
NotificationCompat.Builder builder = new NotificationCompat.Builder(this);
...
builder.setColor(color);
Notification notif = builder.build();
The color is respected only on Lollipop and only affects background of the small icon. If a large icon is shown its contents are entirely your responsibility.
Source: NotificationCompat.Builder#setColor(int)