Here are the basics when it comes to Entering Panama and transiting the Canal. You should budget about $1000 to cover all the fees and expenses, plus of course your food, fuel, marina fees if you don’t want to anchor, etc. It seems that if you are willing to do all the running around and fill out all of the forms on your own, and put up a $800 or so refundable deposit you might get that $1000 down to about $700 or so. Best I can tell there are three options when it comes to preparing to transit the canal. The easiest, smoothest, most expensive way is to hire an agent for around $250 to $500 depending on what agent you get and if they will negotiate. The agent fee is in addition to the transit canal transit fees. Don’t quote me on these numbers but I seem to recall that the Canal fee itself is only $500, but then you have to spend another $100 fee to get ‘measured’ for the canal. The $500 goes up quite a bit if your boats actual length is more than 50 feet. Then there is this “buffer fee” or deposit that most agents can arrange to pay for you, or if you go it alone you have to pay with a credit card or cash that you can get back after the transit. It is to cover any fees you incur if you have problems (engine, crew, etc) during your transit. Then you have to have four lines, I think 150’ each and 3 / 4 inch thick, some people have a few lines on board that meet those specks but usually just rent them anyway for $15 each or $60 for the set of four. Then you have to have around 10 old tires unless you happen to have a zillion huge fenders on board. I think the tires are around $3 each, and then another dollar or two get rid of them on the other side if you can’t find someone who needs them. I ended up paying $600 for the canal fees, plus $350 to the agent, but that covered my lines and tires and a few other fees so I figure Stanley the agent profited about $250 or $300 from me.
The other option (and I think the best one) is to go into the Marina (Panama Canal Yacht Club) and tell them you need to transit the canal. They will probably put you in touch with Tito, he seems to work in the office and does ALMOST everything the agent does for you but for about a tenth of the price ($35-$50). The biggest difference is that you will have to go with him to fill out the forms but he assists you not being a licensed agent he cant exactly do it for you. You will also have to pay your $800 buffer yourself. Basically this will save you several hundred dollars and seems like the obvious way to go unless you are in a huge hurry, hate paperwork, or don’t want to spend half a day running around the deadly (not exaggerating) city of Colon filling out forms.
The last and cheapest option is to do it all on your own. When you check in with immigration at the Yacht Club you can get a vague list of procedures to transit the canal. Find all of the offices, fill out the forms on your own (you almost need to speak Spanish to do this) and deal with the various offices and port captain on your own. In my opinion you would be an idiot to go that route rather than paying Tito at the marina or a local experienced, knowledgeable English-speaking taxi driver to help you.

Plus you have to have four line handlers on your boat during the transit, in addition to the captain, and an advisor / pilot. So this means you will have six people on the boat total, that you will have to provide three meals and snacks and drinks for, plus you will have to sleep five for one night. Generally the advisor boards you boat around 6pm on the night of the transit, you go through the first three locks (Gatun Locks) on the Atlantic side, this gets you into lake Gatun around 11PM where the advisor disembarks and you spend the night. Then around 8am the next morning you motor about 21 miles through like Gatun to the next two sets of locks (three more total) that drop you back down to sea level and into the Pacific, usually around 2PM or so depending on your boat speed and lock availability. They normally send three yachts at a time that raft together while they transit the locks, this makes the line handling easier, the center (and largest) boat usually is the ‘motor’ and steering, while the two smaller boats on the side handle two of the lock-lines each. Basically just taking up slack as you rise up through the locks, and then on the opposite side paying out line as you descend through the locks. Its pretty simple, and most cruisers help each other get through the canal by line-handling for each other. It costs less than $10 for Bus and taxi fairs (about 2.5 hours total) to get from Colon to Panama city, and the transiting yacht covers the food and drinks for their line handlers. A few people who failed to find volunteers to handle the lines hire some Panamanian ‘pros’ for about $100 each. They generally know what they are doing and make the locking an even smoother process, but some people complained that they were a bit crude and disrespectful. Some people even took on back-packers as line handlers which went OK since you only really use two line handlers and you have to have four on board, just be sure you have at least two people that can work and ease a cleat hitch, tie a bowline, etc.
I could write a lot more about the Canal transit but I suppose that’s enough, feel free to email me if you have any questions or even call if its before June 12 th or so at which point I will no longer have a cell phone since I’ll be crossing the Pacific (hopefully).

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