bootstrap had 15px top padding and 15px bottom padding on .navbar-nav > li > a so you need to decrease it by overriding it in your css file and .navbar has min-height:50px; decrease it as much you want.
for example
.navbar-nav > li > a {padding-top:5px !important; padding-bottom:5px !important;}
.navbar {min-height:32px !important}
add these classes to your css and then check.