Transportation from Spain to Portugal

Add a stop in Santiago between Madrid and Porto. It makes the trip between Madrid and Porto very easy and it would be a pity to miss Santiago when you are in the area.

Any particular places you want to see in southern Spain and do you want to include southern Portugal as well?

The ground-transportation link between southern Portugal (the Algarve) and southern Spain (Andalucia) is via bus from Faro to Seville. I am not necessarily recommending the Algarve; I think there are a lot of more interesting places on the Iberian Peninsula, and you don't have a lot of time to cover such a large territory. However, there are few transportation links between the two countries, and the Faro-Seville bus route is one of them.

You can use skyscanner.com to see which Spanish cities you can fly to non-stop from Lisbon if you anticipate that will be your final stop in Portugal. Buy flight tickets directly from the airline. Research baggage and other fees carefully.

One other transportation issue to be aware of is that there isn't a rail link all the way up the east side of Spain from Granada to Barcelona. The fastest route is to take the train back to Madrid and then proceed to Barcelona. If you want to hit some coastal places in between, that means heading back east from Madrid to Valencia; there's fast rail service on that route. Alternatively, you can take a very long bus trip from Granada to Valencia.

When is this trip? Summer heat is likely to be brutal in Andalucia.

You could probably do a mixture of short flights, trains and busses for either a Northern trip or Southern trip. Like others suggested, use skyscanner and both the Spain and Portugal rail sites to plan the trip. Weather - heat would be a deciding factor as well. So, if you have not yet booked your flights from your origin country yet, start in Barcelona for either the Northern loop or the Southern loop.

Southern Loop
Barcelona
Madrid
Granada w/day trip to Cordoba
Seville
Faro
Lisbon

Northern Loop
Barcelona
Madrid
Santiago
Porto
Lisbon

Day trips to Cordoba should be taken from Seville rather than Granada because the travel time is much lower. Cordoba is worth a couple of nights if not more, and it can also be visited in transit between Granada and Seville, which would mean a bit less travel time overall; that may actually be what Linda is suggesting.

I’ve been to Faro and it’s not worth spending time in unless you use it as a transportation hub. Tavira is closer to Sevilla than Faro by 30m. There are direct buses between Sevilla and Tavira (2h) that deserves a two-night stay. There are direct buses from Tavira to Lisbon taking 4h 15m.

Yes Acraven, tour Cordoba Mezquita between Granada and Seville; better not as a day trip

Thank you everyone. I've got a lot to think about. We will be traveling in late September early October. I had hoped the worst of the heat will be over.