<header>

  <a id="title" href="{{ site.url }}">
    <h1>{{ site.title }}</h1>
  </a>

  <ul id="header-page-list">
    {% for page in site.pages %}
      {% if page.title %}
        <a href="{% if site.baseurl == "/" %}{{ page.url }}{% else %}{{ page.url | prepend: site.baseurl }}{% endif %}">
          <h3> {{ page.title }} </h3>
        </a>
      {% endif %}
    {% endfor %}
  </ul>

</header>

<header>

  <a id="title" href="{{ site.url }}">
    <h1>{{ site.title }}</h1>
  </a>

  <ul id="header-page-list">
    {% for page in site.pages %}
      {% if page.title %}
        <a href="{{ page.url | prepend: site.url }}">
          <h3> {{ page.title }} </h3>
        </a>
      {% endif %}
    {% endfor %}
  </ul>

</header>

Use site.url to create page URL
Use site.url to create page URL
